3L2P.A | LIG3 – ASTRID

3L2P.A | LIG3

General Structure Information

PDB ID	3l2p
HGNC Gene Label(s)	LIG3
Structure Name	human dna ligase iii recognizes dna ends by dynamic switching between two dna bound states
Resolution	3.0Å
Reference	AUTH E.COTNER-GOHARA,I.K.KIM,M.HAMMEL,J.A.TAINER,A.E.TOMKINSON,AUTH 2 T.ELLENBERGERTITL HUMAN DNA LIGASE III RECOGNIZES DNA ENDS BY DYNAMICTITL 2 SWITCHING BETWEEN TWO DNA-BOUND STATES.REF BIOCHEMISTRY V. 49 6165 2010REFN ISSN 0006-2960PMID 20518483DOI 10.1021/BI100503W

Variant Set Distributions

ExAC Variants

Number Of Residues	533
Number Of SNVs	129
Number Of Permutations	22411
Optimal Distance Threshold	16.0
K Statistic	0.094
p-value	0.161

COSMIC

Number Of Residues	533
Number Of SNVs	7
Number Of Permutations	5605
Optimal Distance Threshold	7.0
K Statistic	0.048
p-value	0.581

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	129
Number Of COSMIC SNVs	7
Optimal Distance Threshold	7.0
K Statistic	0.034
p-value	0.702

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:33316562		R>W	A:170	(34.67, -6.13, 65.58)
17:33316583	rs141255794	R>W	A:177	(33.68, -6.04, 52.32)
17:33316584	rs149175581	R>Q	A:177	(33.68, -6.04, 52.32)
17:33316593		R>Q	A:180	(31.23, -0.68, 49.90)
17:33316604		A>T	A:184	(25.14, -1.01, 46.33)
17:33316609		M>I	A:185	(22.15, -3.86, 47.51)
17:33316620		N>I	A:189	(16.75, -1.86, 43.93)
17:33316626		S>T	A:191	(11.80, 0.03, 44.56)
17:33316632		N>S	A:193	(8.77, -0.39, 48.71)
17:33316641		T>I	A:196	(13.23, 0.21, 52.95)
17:33316657		D>E	A:201	(16.38, -7.15, 55.88)
17:33316662		L>P	A:203	(18.99, -2.89, 60.61)
17:33316664		R>W	A:204	(14.87, -6.33, 61.58)
17:33316665	rs199806002	R>Q	A:204	(14.87, -6.33, 61.58)
17:33317993	rs376449090	G>S	A:214	(25.63, -3.84, 65.15)
17:33317996		D>N	A:215	(26.15, 0.68, 65.36)
17:33317999		V>M	A:216	(21.94, 1.13, 64.88)
17:33318021		L>P	A:223	(22.64, 5.41, 55.37)
17:33318029		G>R	A:226	(22.16, 14.95, 53.76)
17:33318032		V>I	A:227	(19.88, 14.54, 56.54)
17:33318059	rs148073351	D>N	A:236	(34.49, 19.04, 43.43)
17:33318060		D>G	A:236	(34.49, 19.04, 43.43)
17:33318065		Q>E	A:238	(40.21, 22.36, 47.42)
17:33318071	rs141783152	V>L	A:240	(41.30, 17.67, 43.07)
17:33318084	rs556444691	S>I	A:244	(47.34, 16.05, 43.59)
17:33318086		R>C	A:245	(49.07, 18.72, 46.86)
17:33318098		C>R	A:249	(49.37, 13.73, 40.20)
17:33318110	rs150154135	D>N	A:253	(44.72, 15.06, 34.16)
17:33318120	rs370882864	R>Q	A:256	(39.89, 16.99, 30.30)
17:33318696		V>M	A:263	(34.74, 13.51, 42.78)
17:33318742		P>L	A:278	(49.38, 2.57, 47.36)
17:33318744	rs368652393 COSM3937329 COSM3937328	P>A	A:279	(45.73, 1.16, 47.16)
17:33318748		A>G	A:280	(44.88, -1.02, 50.49)
17:33318750		A>S	A:281	(45.11, -4.69, 50.60)
17:33318751		A>V	A:281	(45.11, -4.69, 50.60)
17:33318777		V>M	A:290	(34.57, 6.57, 59.00)
17:33318781		D>G	A:291	(32.15, 8.99, 62.62)
17:33318795	rs201706144	R>W	A:296	(40.61, 14.26, 62.06)
17:33318796	rs192558553	R>Q	A:296	(40.61, 14.26, 62.06)
17:33318841		Q>R	A:311	(47.76, 10.90, 53.68)
17:33318988	rs375415869	N>S	A:320	(36.14, 0.22, 46.71)
17:33319021		H>R	A:331	(27.26, 16.08, 51.91)
17:33319024		D>G	A:332	(25.43, 12.17, 47.55)
17:33319051		H>R	A:341	(12.61, 5.85, 51.62)
17:33319548		D>G	A:344	(10.52, 3.77, 56.87)
17:33319562		N>D	A:349	(6.31, 6.03, 63.17)
17:33319572		E>A	A:352	(5.52, 11.11, 61.74)
17:33319577		F>I	A:354	(13.74, 13.12, 62.20)
17:33319587	COSM705540 COSM705539	S>L	A:357	(12.04, 15.54, 66.98)
17:33319590	rs567712080 COSM977784 COSM977783	R>H	A:358	(15.57, 17.24, 62.16)
17:33319602		D>V	A:362	(16.07, 10.78, 70.56)
17:33319604	rs536339528	V>M	A:363	(14.80, 8.46, 67.15)
17:33319614		R>Q	A:366	(12.31, 7.62, 70.99)
17:33319628	rs547119482	A>T	A:371	(13.01, -3.06, 71.17)
17:33319637		V>M	A:374	(9.42, -7.76, 73.65)
17:33319673	COSM1256463 COSM1256462	V>I	A:386	(4.87, 11.34, 66.72)
17:33319683	COSM3819303 COSM3819302	S>L	A:389	(10.89, 18.16, 71.94)
17:33319704		P>H	A:396	(9.62, 23.28, 58.95)
17:33319706		M>V	A:397	(4.40, 23.50, 57.72)
17:33321298		E>K	A:400	(1.78, 23.67, 46.90)
17:33321300		E>D	A:400	(1.78, 23.67, 46.90)
17:33321311	COSM3516151 COSM3516150	S>F	A:404	(-5.04, 28.79, 40.56)
17:33321313	rs142785435	V>I	A:405	(-8.03, 30.95, 42.46)
17:33321325	rs371160625	M>V	A:409	(-11.03, 27.61, 46.74)
17:33321326		M>T	A:409	(-11.03, 27.61, 46.74)
17:33321341		N>S	A:414	(-12.64, 24.66, 55.38)
17:33321342		N>K	A:414	(-12.64, 24.66, 55.38)
17:33321348	rs532596955	M>I	A:416	(-8.44, 30.68, 53.11)
17:33321353		S>C	A:418	(-4.37, 35.56, 53.87)
17:33321367		D>N	A:423	(11.25, 38.33, 51.22)
17:33321389		H>R	A:430	(12.49, 26.39, 70.20)
17:33321394		N>D	A:432	(13.11, 26.60, 78.39)
17:33321422	rs145992710	R>H	A:441	(13.55, 25.61, 55.39)
17:33321431		K>M	A:444	(21.48, 25.21, 59.86)
17:33321436		V>I	A:446	(19.86, 31.83, 63.43)
17:33321443		P>L	A:448	(23.79, 35.38, 66.07)
17:33323098	rs147386726	D>N	A:456	(15.43, 41.53, 75.41)
17:33323120		P>L	A:463	(3.09, 37.59, 78.99)
17:33323123		G>E	A:464	(3.60, 33.75, 80.90)
17:33323132		S>T	A:467	(7.36, 27.34, 77.24)
17:33323136		M>I	A:468	(7.33, 29.32, 73.67)
17:33323162		I>T	A:477	(11.82, 46.80, 59.96)
17:33323164		D>Y	A:478	(12.37, 51.34, 57.80)
17:33323167		N>D	A:479	(12.22, 52.04, 62.74)
17:33323170	rs200503859	K>Q	A:480	(11.01, 55.56, 60.03)
17:33323206		V>L	A:492	(26.21, 41.87, 58.89)
17:33323600	rs149469889	A>D	A:497	(23.97, 50.77, 56.28)
17:33323605	rs535499838	Q>E	A:499	(20.19, 54.44, 60.44)
17:33323606	COSM436382 COSM436381	Q>R	A:499	(20.19, 54.44, 60.44)
17:33323621		C>Y	A:504	(11.43, 42.13, 62.93)
17:33323639		C>F	A:510	(1.96, 28.34, 68.05)
17:33323644		Y>H	A:512	(5.40, 23.54, 73.11)
17:33323672	rs200267761	R>K	A:521	(-4.59, 22.09, 69.49)
17:33324766		C>W	A:524	(-8.48, 28.35, 63.96)
17:33324768	rs201705066	E>V	A:525	(-7.74, 26.30, 68.23)
17:33324771	rs546806092	R>Q	A:526	(-2.62, 26.86, 65.58)
17:33324773	COSM3672410 COSM3672409	R>W	A:527	(-5.63, 33.77, 64.53)
17:33324780		F>Y	A:529	(-3.14, 30.40, 72.60)
17:33324789		D>A	A:532	(-5.91, 35.07, 73.41)
17:33324792	rs188532751	N>S	A:533	(-1.50, 34.36, 74.92)
17:33324803		I>V	A:537	(6.75, 44.70, 70.81)
17:33324813		R>Q	A:540	(12.24, 44.51, 67.50)
17:33325253		A>S	A:556	(-8.51, 37.61, 43.35)
17:33325268		R>W	A:561	(-5.39, 44.24, 47.78)
17:33325290		E>V	A:568	(7.35, 39.25, 47.03)
17:33325308		D>G	A:574	(-7.24, 25.40, 55.70)
17:33325310		V>M	A:575	(-9.14, 27.32, 58.76)
17:33325623		G>S	A:577	(-5.50, 23.07, 60.00)
17:33325629		Y>H	A:579	(2.60, 22.69, 62.23)
17:33325632		E>K	A:580	(1.04, 18.73, 58.81)
17:33325644		R>G	A:584	(5.46, 21.64, 50.26)
17:33325645		R>Q	A:584	(5.46, 21.64, 50.26)
17:33325668	COSM3819309 COSM3819308	D>Y	A:592	(5.77, 34.21, 39.01)
17:33325672		Y>C	A:593	(3.84, 30.84, 40.84)
17:33325692		A>P	A:600	(6.06, 37.44, 34.55)
17:33325701		A>P	A:603	(13.82, 37.70, 29.29)
17:33325707		L>V	A:605	(18.25, 36.36, 27.24)
17:33325729	COSM4065513 COSM4065512	Y>C	A:612	(31.05, 20.08, 31.36)
17:33325741		S>N	A:616	(22.65, 12.44, 36.39)
17:33326328	COSM3516155 COSM3516154	G>S	A:619	(29.16, 15.62, 30.10)
17:33326332		M>K	A:620	(25.83, 16.76, 29.67)
17:33326361	COSM32324	D>N	A:630	(25.87, 46.67, 24.58)
17:33326375		Q>H	A:634	(29.10, 47.62, 19.80)
17:33326381		W>C	A:636	(27.72, 39.67, 22.47)
17:33326413		D>A	A:647	(13.03, 18.00, 28.88)
17:33326415		D>N	A:648	(16.14, 14.74, 30.16)
17:33326422	rs146586818	T>M	A:650	(15.27, 18.97, 25.32)
17:33326430		R>C	A:653	(17.13, 18.65, 20.50)
17:33326449		D>G	A:659	(27.83, 26.71, 18.47)
17:33326454		V>L	A:661	(32.38, 28.05, 23.64)
17:33328298		T>I	A:698	(11.27, 33.24, 33.89)
17:33328300		G>R	A:699	(11.38, 35.21, 37.37)
17:33328307		E>A	A:701	(12.36, 39.66, 41.51)
17:33328313		S>F	A:703	(18.70, 41.24, 40.55)
17:33328325		A>V	A:707	(28.55, 40.24, 39.06)
17:33328337		D>A	A:711	(25.04, 47.13, 35.25)
17:33328370		R>Q	A:722	(10.22, 29.68, 26.06)
17:33328372		I>V	A:723	(12.00, 27.18, 22.95)
17:33328393		K>E	A:730	(18.30, 41.67, 17.51)
17:33328394		K>R	A:730	(18.30, 41.67, 17.51)

3L2P.A | LIG3.

3L2P.A | LIG3

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

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
17:33318996	COSM1610076	K>Q	A:323	(34.12, 5.83, 45.50)
17:33319005	COSM1610079	I>L	A:326	(34.77, 10.98, 48.73)
17:33319550	COSM977780	A>T	A:345	(13.76, 0.59, 58.35)
17:33319629	COSM977786	A>V	A:371	(13.01, -3.06, 71.17)
17:33321436	COSM4697962	V>I	A:446	(19.86, 31.83, 63.43)
17:33326361	COSM32324	D>N	A:630	(25.87, 46.67, 24.58)
17:33328285	COSM3181093	V>M	A:694	(17.17, 33.13, 21.65)