4CGY.A | TOP3A

General Structure Information

PDB ID	4cgy
HGNC Gene Label(s)	TOP3A
Structure Name	crystal structure of the human topoisomerase iii alpha-rmi1 complex
Resolution	2.85Å
Reference	AUTH N.BOCQUET,A.H.BIZARD,W.ABDULRAHMAN,N.B.LARSEN,M.FATY,AUTH 2 S.CAVADINI,R.D.BUNKER,S.C.KOWALCZYKOWSKI,P.CEJKA,AUTH 3 I.D.HICKSON,N.H.THOMATITL STRUCTURAL AND MECHANISTIC INSIGHT INTO HOLLIDAY-JUNCTIONTITL 2 DISSOLUTION BY TOPOISOMERASE IIIALPHA AND RMI1REF NAT.STRUCT.MOL.BIOL. V. 21 261 2014REFN ISSN 1545-9993PMID 24509834DOI 10.1038/NSMB.2775

Variant Set Distributions

ExAC Variants

Number Of Residues	619
Number Of SNVs	165
Number Of Permutations	80715
Optimal Distance Threshold	6.0
K Statistic	0.006
p-value	0.063

COSMIC

Number Of Residues	619
Number Of SNVs	6
Number Of Permutations	1976
Optimal Distance Threshold	6.0
K Statistic	0.067
p-value	0.526

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	165
Number Of COSMIC SNVs	5
Optimal Distance Threshold	26.0
K Statistic	-0.243
p-value	0.618

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:18218031		F>S	A:21	(-21.56, -3.28, 64.73)
17:18218007	COSM1749893	A>V	A:29	(-13.20, -0.74, 70.15)
17:18217999		G>C	A:32	(-7.64, 3.52, 73.86)
17:18217992		R>Q	A:34	(-4.08, 7.21, 72.34)
17:18217975		A>T	A:40	(-7.80, 10.29, 51.40)
17:18217959	rs559137278	A>V	A:45	(-10.34, 15.54, 50.30)
17:18217944	rs551758837	A>G	A:50	(-10.80, 18.22, 58.02)
17:18217928	rs370459618	N>K	A:55	(-15.74, 23.88, 62.40)
17:18212246	rs150497993	L>V	A:64	(7.57, 12.24, 54.08)
17:18212236		F>S	A:67	(2.44, 17.84, 46.37)
17:18212233	rs200695657	N>S	A:68	(0.28, 14.33, 50.24)
17:18212224		Y>C	A:71	(-4.72, 18.48, 57.04)
17:18212221		E>G	A:72	(-3.22, 16.81, 63.90)
17:18212209		H>P	A:76	(-16.24, 12.50, 70.75)
17:18212206		L>Q	A:77	(-14.86, 8.69, 67.38)
17:18211737		N>S	A:81	(-12.13, 12.50, 73.16)
17:18211732	rs550633885 COSM4064516	T>A	A:83	(-6.12, 13.14, 67.60)
17:18211728		M>T	A:84	(-8.75, 12.79, 63.65)
17:18211723		M>V	A:86	(-6.95, 13.59, 57.63)
17:18211711		S>A	A:90	(-2.21, 10.40, 45.02)
17:18211704		H>R	A:92	(-4.53, 3.44, 42.66)
17:18211700		L>F	A:93	(-0.04, 3.63, 46.89)
17:18211692		H>R	A:96	(-0.80, -3.40, 37.98)
17:18211681	rs376902371	M>V	A:100	(12.34, -7.69, 35.95)
17:18211671	COSM1268309	R>Q	A:103	(8.81, -6.03, 34.01)
17:18210276	rs558756856	S>G	A:107	(11.92, -12.30, 27.85)
17:18210270		N>D	A:109	(5.96, -16.27, 23.91)
17:18210264		L>V	A:111	(1.18, -17.77, 25.29)
17:18210260		V>G	A:112	(3.91, -16.94, 28.96)
17:18210258	rs369250015	L>F	A:113	(2.17, -12.92, 29.63)
17:18210242		I>S	A:118	(1.28, -10.65, 38.50)
17:18210234		Y>H	A:121	(5.27, -1.67, 41.64)
17:18210228		P>S	A:123	(5.57, 3.65, 42.73)
17:18210218		F>C	A:126	(3.05, 7.24, 44.56)
17:18208533		K>I	A:131	(8.26, 6.06, 54.28)
17:18208521	rs117400470	R>Q	A:135	(5.57, 9.38, 59.78)
17:18208512	rs576988479	R>H	A:138	(5.42, 3.63, 63.21)
17:18208513		R>C	A:138	(5.42, 3.63, 63.21)
17:18208500		A>V	A:142	(-6.77, 3.50, 64.19)
17:18208480		C>R	A:149	(-17.56, 5.54, 47.77)
17:18208471		E>K	A:152	(-10.95, 1.88, 41.66)
17:18208465	COSM4064515	E>K	A:154	(-13.06, -0.02, 48.86)
17:18206034		K>M	A:168	(0.25, -1.35, 64.03)
17:18206029		N>D	A:170	(-3.21, -6.36, 65.56)
17:18206021	rs144079378	Q>H	A:172	(-9.41, -0.87, 64.95)
17:18206022	rs368048718	Q>L	A:172	(-9.41, -0.87, 64.95)
17:18206015		L>F	A:174	(-12.96, 1.47, 60.56)
17:18206013	rs200654584	R>Q	A:175	(-14.85, 3.02, 54.26)
17:18205981	COSM182181	V>I	A:186	(-18.56, 14.20, 57.12)
17:18205960		L>V	A:193	(-17.52, 4.02, 60.96)
17:18205952		E>D	A:195	(-15.98, -4.27, 57.62)
17:18205954		E>K	A:195	(-15.98, -4.27, 57.62)
17:18205940		R>S	A:199	(-17.63, -9.51, 48.71)
17:18205933	rs117856165	D>N	A:202	(-11.19, -8.89, 45.35)
17:18205921	rs377762117	V>M	A:206	(-9.88, -9.59, 38.77)
17:18205911	rs557164714	E>V	A:209	(-4.85, -10.31, 36.93)
17:18205745		A>G	A:216	(0.33, -7.89, 27.02)
17:18205739		F>S	A:218	(-3.95, -10.16, 22.33)
17:18205718		R>Q	A:225	(3.17, -10.45, 12.61)
17:18205706		I>T	A:229	(4.96, -7.22, 8.15)
17:18205695		V>M	A:233	(3.93, 2.34, 8.14)
17:18205668		G>S	A:242	(-8.03, -4.20, 24.59)
17:18205643		G>D	A:250	(-16.07, -1.71, 16.46)
17:18205628		R>Q	A:255	(-22.61, 3.62, 12.53)
17:18205624		F>L	A:256	(-16.90, 3.81, 7.74)
17:18205578	rs369508573	V>L	A:272	(-50.79, 19.21, -0.09)
17:18205293		H>R	A:274	(-54.29, 26.15, 2.42)
17:18205274	rs34430764	I>M	A:280	(-47.74, 27.98, 4.53)
17:18205254		R>M	A:287	(-50.69, 6.22, 0.22)
17:18205248		R>L	A:289	(-41.41, 7.48, 1.93)
17:18205246	rs544579350	L>I	A:290	(-44.28, 5.65, -3.06)
17:18205200		E>V	A:305	(-57.91, 14.90, -12.43)
17:18202940		M>T	A:308	(-61.90, 20.61, -3.65)
17:18202938		A>T	A:309	(-60.37, 19.68, -0.17)
17:18202929		V>I	A:312	(-62.46, 14.05, 7.03)
17:18202923		V>I	A:314	(-61.09, 17.98, 13.39)
17:18202917	rs368476765	S>T	A:316	(-57.86, 17.21, 19.71)
17:18202912		K>N	A:317	(-54.82, 14.12, 21.33)
17:18202899		W>R	A:322	(-42.64, 12.02, 29.86)
17:18202886		A>V	A:326	(-32.85, 11.20, 37.52)
17:18202881		D>Y	A:328	(-27.22, 8.67, 35.59)
17:18202878		T>A	A:329	(-22.74, 9.01, 35.16)
17:18202875		V>L	A:330	(-24.50, 7.69, 31.36)
17:18198084		A>P	A:336	(-22.50, 17.31, 28.15)
17:18198077	rs145416998	R>Q	A:338	(-26.90, 15.76, 23.14)
17:18198068	rs149870245	R>K	A:341	(-20.97, 22.24, 22.83)
17:18198039		A>T	A:351	(-17.56, 16.43, 38.53)
17:18196162	rs202043817	I>L	A:360	(-21.82, 17.80, 43.04)
17:18196147		T>S	A:365	(-24.01, 6.85, 40.02)
17:18196137	rs543070592	N>S	A:368	(-32.30, 6.59, 38.24)
17:18196110	COSM976287	T>M	A:377	(-37.53, 20.48, 50.21)
17:18196092		Q>R	A:383	(-30.37, 26.47, 44.28)
17:18196087	rs139068958	P>S	A:385	(-30.40, 32.25, 46.15)
17:18196084		D>N	A:386	(-29.77, 31.99, 41.31)
17:18196081		P>A	A:387	(-30.35, 35.14, 39.76)
17:18196077	COSM704808	R>H	A:388	(-29.07, 32.26, 36.93)
17:18196078		R>C	A:388	(-29.07, 32.26, 36.93)
17:18196068		A>V	A:391	(-37.86, 31.63, 40.84)
17:18196055	rs529651014	S>R	A:395	(-42.25, 27.44, 41.98)
17:18196044	rs140080915	R>Q	A:399	(-46.48, 24.92, 41.55)
17:18196045	rs61756259	R>W	A:399	(-46.48, 24.92, 41.55)
17:18196041	rs146192054	G>D	A:400	(-45.72, 21.76, 47.45)
17:18196042		G>S	A:400	(-45.72, 21.76, 47.45)
17:18196039	COSM704809	G>C	A:401	(-43.01, 20.50, 46.00)
17:18196036		P>S	A:402	(-40.29, 18.38, 45.71)
17:18196027	rs76300532	R>C	A:405	(-38.74, 11.21, 35.26)
17:18196023		N>S	A:406	(-37.64, 8.63, 40.06)
17:18195978		K>R	A:421	(-23.02, 24.32, 48.57)
17:18195976		Y>H	A:422	(-25.88, 28.90, 45.41)
17:18195966		N>S	A:425	(-18.19, 31.90, 43.26)
17:18195967		N>D	A:425	(-18.19, 31.90, 43.26)
17:18195964		L>V	A:426	(-18.37, 28.37, 39.63)
17:18194337		D>G	A:429	(-16.51, 24.44, 31.41)
17:18194319		E>G	A:435	(-26.20, 26.20, 34.91)
17:18194320		E>K	A:435	(-26.20, 26.20, 34.91)
17:18194296		A>S	A:443	(-36.69, 19.79, 36.16)
17:18194289		C>S	A:445	(-38.32, 18.25, 41.03)
17:18194290		C>R	A:445	(-38.32, 18.25, 41.03)
17:18194268	rs535654822	Q>R	A:452	(-54.03, 21.39, 22.53)
17:18194248	rs28671051	D>N	A:459	(-60.15, 13.56, 0.67)
17:18194245	rs141787612	I>V	A:460	(-57.34, 15.46, -2.37)
17:18194234		E>D	A:463	(-55.49, 10.04, -1.75)
17:18194215		L>F	A:470	(-48.40, 22.13, 19.49)
17:18194212		M>V	A:471	(-51.67, 25.07, 22.17)
17:18194199	rs144590444	R>Q	A:475	(-42.86, 26.05, 28.32)
17:18194185		V>M	A:480	(-35.32, 25.43, 34.43)
17:18194181		Y>F	A:481	(-33.64, 21.19, 30.90)
17:18194173		D>N	A:484	(-35.25, 20.17, 26.36)
17:18193994		P>S	A:492	(-55.47, 27.27, 10.95)
17:18193987	rs138286093	Y>C	A:494	(-58.87, 23.89, 8.67)
17:18193972	rs147048688	H>P	A:499	(-65.81, 21.61, 1.06)
17:18193969		F>C	A:500	(-59.58, 23.33, 1.27)
17:18193960		S>T	A:503	(-51.88, 26.49, -2.90)
17:18193955		V>M	A:505	(-50.78, 19.84, -5.78)
17:18193946		V>M	A:508	(-41.84, 16.13, -4.45)
17:18193940		G>R	A:510	(-36.35, 11.90, -2.71)
17:18193930		S>I	A:513	(-30.36, 9.12, 4.32)
17:18193910	rs367956874	E>K	A:520	(-18.53, 10.82, 23.23)
17:18193892		L>F	A:526	(-23.67, 1.42, 21.20)
17:18188825		A>V	A:536	(-17.93, 4.80, 34.89)
17:18188820		H>Y	A:538	(-18.40, 4.40, 29.40)
17:18188816	COSM976285	A>V	A:539	(-14.21, 7.71, 28.79)
17:18188808		I>V	A:542	(-13.83, 6.72, 24.22)
17:18188789	rs151096656	R>Q	A:548	(-2.87, 4.19, 21.67)
17:18188790		R>W	A:548	(-2.87, 4.19, 21.67)
17:18188785		M>I	A:549	(-3.98, 7.84, 16.48)
17:18188771		T>N	A:554	(-15.06, 14.59, 12.28)
17:18188765		D>V	A:556	(-19.98, 16.95, 12.61)
17:18188759		R>Q	A:558	(-20.21, 12.72, 13.99)
17:18188760	rs377076547 COSM182171	R>W	A:558	(-20.21, 12.72, 13.99)
17:18188747		G>E	A:562	(-8.42, 4.36, 10.75)
17:18188743	rs529652900	H>Q	A:563	(-6.26, 3.45, 7.10)
17:18188735		M>T	A:566	(-10.75, -0.30, 9.44)
17:18188729		L>P	A:568	(-6.64, -4.19, 13.70)
17:18188730		L>F	A:568	(-6.64, -4.19, 13.70)
17:18188721		G>S	A:571	(-8.78, -9.06, 10.64)
17:18188608		M>I	A:575	(-9.42, -14.55, 12.15)
17:18188600	rs143808897	E>A	A:578	(-17.19, -12.08, 14.98)
17:18188589		P>S	A:582	(-19.33, -6.72, 22.75)
17:18188582	rs34001746	L>R	A:584	(-15.83, -11.98, 25.57)
17:18188580		R>W	A:585	(-14.86, -6.24, 28.93)
17:18188574	rs146664233	E>Q	A:587	(-19.32, -12.64, 29.22)
17:18188543		D>V	A:597	(-22.80, -8.98, 44.61)
17:18188536		K>N	A:599	(-23.77, -13.40, 43.46)
17:18188537		K>R	A:599	(-23.77, -13.40, 43.46)
17:18188528		K>R	A:602	(-10.96, -13.96, 43.59)
17:18188522		V>A	A:604	(-13.89, -19.03, 38.96)
17:18188501		Q>R	A:611	(-9.26, -19.66, 29.16)
17:18188496		Y>H	A:613	(-10.00, -13.10, 26.50)
17:18188480		I>T	A:618	(-4.19, -19.87, 20.65)
17:18188474	COSM704811	A>V	A:620	(-4.98, -15.30, 16.40)
17:18188472		V>M	A:621	(-1.32, -16.78, 16.69)
17:18188469	rs543109098	A>T	A:622	(-2.95, -19.21, 13.74)
17:18188458		K>N	A:625	(-0.67, -14.74, 7.52)
17:18186148	rs139844084	E>K	A:629	(-4.28, -10.64, 4.42)
17:18186144		A>G	A:630	(-6.31, -6.21, 6.20)
17:18186142		L>V	A:631	(-3.45, -3.69, 7.55)
17:18186117		T>I	A:639	(8.45, -8.47, 4.35)

4CGY.A | TOP3A.

4CGY.A | TOP3A

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants