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Zinc in PDB 2v89: Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution

Protein crystallography data

The structure of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution, PDB code: 2v89 was solved by S.Ramon-Maiques, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.978, 46.807, 56.808, 90.00, 106.78, 90.00
R / Rfree (%) 12.3 / 15.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution (pdb code 2v89). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution, PDB code: 2v89:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2v89

Go back to Zinc Binding Sites List in 2v89
Zinc binding site 1 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2488

b:10.7
occ:1.00
HD1 A:HIS1455 1.2 11.5 1.0
ND1 A:HIS1455 2.1 9.6 1.0
SG A:CYS1423 2.3 13.2 1.0
SG A:CYS1419 2.3 12.0 1.0
SG A:CYS1458 2.3 12.5 1.0
HB2 A:HIS1455 2.8 11.5 1.0
HB2 A:CYS1423 3.0 17.1 1.0
CE1 A:HIS1455 3.0 10.3 1.0
HB3 A:CYS1419 3.1 15.4 1.0
CG A:HIS1455 3.1 9.3 1.0
CB A:CYS1423 3.2 14.2 1.0
HE1 A:HIS1455 3.2 12.4 1.0
H A:CYS1419 3.2 16.9 1.0
HB2 A:CYS1458 3.2 14.5 1.0
CB A:CYS1458 3.3 12.1 1.0
CB A:CYS1419 3.3 12.8 1.0
HA A:CYS1423 3.3 19.0 1.0
CB A:HIS1455 3.5 9.6 1.0
H A:HIS1455 3.5 11.4 1.0
HB3 A:CYS1458 3.5 14.5 1.0
HB A:VAL1425 3.5 24.4 1.0
HG21 A:VAL1425 3.6 34.7 1.0
HG22 A:VAL1425 3.8 34.7 1.0
CA A:CYS1423 3.8 15.8 1.0
H A:VAL1425 3.9 29.5 1.0
N A:CYS1419 3.9 14.1 1.0
H A:ASP1424 4.0 29.8 1.0
HB3 A:CYS1423 4.0 17.1 1.0
CG2 A:VAL1425 4.0 23.1 1.0
HB2 A:CYS1419 4.1 15.4 1.0
HB3 A:HIS1455 4.1 11.5 1.0
CA A:CYS1419 4.1 13.7 1.0
N A:HIS1455 4.2 9.5 1.0
NE2 A:HIS1455 4.2 9.8 1.0
CB A:VAL1425 4.2 20.3 1.0
CD2 A:HIS1455 4.3 9.8 1.0
CA A:HIS1455 4.4 9.4 1.0
H A:CYS1420 4.5 16.5 1.0
N A:ASP1424 4.5 24.9 1.0
C A:CYS1423 4.5 20.2 1.0
N A:VAL1425 4.6 24.6 1.0
H A:CYS1458 4.7 13.8 1.0
CA A:CYS1458 4.7 12.2 1.0
C A:CYS1419 4.8 13.8 1.0
HA A:THR1418 4.8 19.9 1.0
N A:CYS1420 4.8 13.8 1.0
SG A:CYS1420 4.9 16.5 1.0
O A:ILE1417 4.9 16.1 1.0
HG23 A:VAL1425 4.9 34.7 1.0
HA A:CYS1419 5.0 16.4 1.0
N A:CYS1423 5.0 17.8 1.0
O A:HIS1455 5.0 9.7 1.0
HA A:CYS1458 5.0 14.6 1.0

Zinc binding site 2 out of 4 in 2v89

Go back to Zinc Binding Sites List in 2v89
Zinc binding site 2 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2489

b:9.3
occ:1.00
HD1 A:HIS1481 1.2 13.3 1.0
NE2 A:HIS1452 2.0 9.3 1.0
ND1 A:HIS1481 2.0 11.1 1.0
SG A:CYS1446 2.3 9.3 1.0
SG A:CYS1478 2.3 11.5 1.0
CE1 A:HIS1481 3.0 12.5 1.0
HB2 A:HIS1481 3.0 12.2 1.0
CE1 A:HIS1452 3.0 10.3 1.0
CD2 A:HIS1452 3.0 10.8 1.0
HE1 A:HIS1481 3.1 15.1 1.0
CG A:HIS1481 3.1 10.9 1.0
HB3 A:CYS1446 3.1 10.7 1.0
CB A:CYS1446 3.2 8.9 1.0
HB3 A:CYS1478 3.2 12.1 1.0
HE1 A:HIS1452 3.2 12.3 1.0
HD2 A:HIS1452 3.2 12.9 1.0
H A:CYS1478 3.2 12.2 1.0
HB2 A:CYS1446 3.3 10.7 1.0
HB3 A:HIS1448 3.4 13.4 1.0
CB A:CYS1478 3.4 10.1 1.0
CB A:HIS1481 3.5 10.2 1.0
HB2 A:HIS1448 3.9 13.4 1.0
N A:CYS1478 3.9 10.2 1.0
HB3 A:HIS1481 4.1 12.2 1.0
CB A:HIS1448 4.1 11.2 1.0
NE2 A:HIS1481 4.1 13.3 1.0
HB2 A:CYS1478 4.1 12.1 1.0
ND1 A:HIS1452 4.1 9.8 1.0
CG A:HIS1452 4.2 9.8 1.0
CD2 A:HIS1481 4.2 13.0 1.0
CA A:CYS1478 4.2 10.0 1.0
H A:HIS1481 4.2 13.4 1.0
HB2 A:GLU1480 4.2 17.4 0.5
H A:HIS1448 4.3 11.6 1.0
N A:HIS1481 4.5 11.2 1.0
CA A:CYS1446 4.6 8.3 1.0
CA A:HIS1481 4.7 11.6 1.0
HA A:TYR1477 4.7 11.2 1.0
HG12 A:VAL1454 4.7 15.8 1.0
HG13 A:VAL1454 4.7 15.8 1.0
C A:CYS1478 4.8 9.8 1.0
CG A:HIS1448 4.8 12.4 1.0
O A:HOH2127 4.9 25.2 1.0
HD2 A:HIS1448 4.9 18.3 1.0
HD1 A:HIS1452 4.9 11.8 1.0
H A:GLU1480 4.9 17.1 1.0
O A:CYS1478 5.0 11.6 1.0
HA A:CYS1446 5.0 10.0 1.0

Zinc binding site 3 out of 4 in 2v89

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Zinc binding site 3 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1488

b:7.4
occ:1.00
HD1 B:HIS455 1.2 9.4 1.0
ND1 B:HIS455 2.1 7.8 1.0
SG B:CYS419 2.3 9.0 1.0
SG B:CYS423 2.3 9.3 1.0
SG B:CYS458 2.3 8.4 1.0
HB2 B:HIS455 2.8 9.4 1.0
CE1 B:HIS455 3.1 8.5 1.0
HB3 B:CYS419 3.1 12.5 1.0
CG B:HIS455 3.1 6.9 1.0
HB2 B:CYS423 3.1 11.4 1.0
H B:CYS419 3.2 13.0 1.0
HB2 B:CYS458 3.2 8.4 1.0
CB B:CYS423 3.2 9.5 1.0
HE1 B:HIS455 3.2 10.2 1.0
HA B:CYS423 3.3 11.4 1.0
CB B:CYS458 3.3 7.0 1.0
CB B:CYS419 3.3 10.4 1.0
CB B:HIS455 3.4 7.8 1.0
HB B:VAL425 3.4 17.2 1.0
HB3 B:CYS458 3.5 8.4 1.0
H B:HIS455 3.5 8.4 1.0
H B:VAL425 3.5 13.1 1.0
HG21 B:VAL425 3.7 20.8 1.0
CA B:CYS423 3.7 9.5 1.0
H B:ASP424 3.8 14.1 1.0
N B:CYS419 3.9 10.8 1.0
HB2 B:CYS419 4.0 12.5 1.0
HG22 B:VAL425 4.1 20.8 1.0
HB3 B:HIS455 4.1 9.4 1.0
HB3 B:CYS423 4.1 11.4 1.0
CA B:CYS419 4.1 10.9 1.0
CG2 B:VAL425 4.2 13.9 1.0
N B:HIS455 4.2 7.0 1.0
CB B:VAL425 4.2 14.3 1.0
NE2 B:HIS455 4.2 8.0 1.0
CD2 B:HIS455 4.2 7.8 1.0
N B:ASP424 4.3 11.7 1.0
N B:VAL425 4.4 10.9 1.0
CA B:HIS455 4.4 7.5 1.0
C B:CYS423 4.4 10.9 1.0
H B:CYS420 4.5 11.5 1.0
H B:CYS458 4.6 9.1 1.0
CA B:CYS458 4.7 7.3 1.0
HA B:THR418 4.8 17.5 1.0
C B:CYS419 4.8 11.3 1.0
N B:CYS420 4.9 9.6 1.0
SG B:CYS420 4.9 11.3 1.0
O B:HIS455 4.9 7.6 1.0
O B:ILE417 4.9 13.8 1.0
CA B:VAL425 4.9 12.3 1.0
HA B:CYS419 5.0 13.1 1.0
N B:CYS423 5.0 10.3 1.0

Zinc binding site 4 out of 4 in 2v89

Go back to Zinc Binding Sites List in 2v89
Zinc binding site 4 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide at 1.1A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1489

b:8.2
occ:1.00
HD1 B:HIS481 1.2 12.8 1.0
NE2 B:HIS452 2.0 7.6 1.0
ND1 B:HIS481 2.1 10.7 1.0
SG B:CYS478 2.3 10.5 1.0
SG B:CYS446 2.3 8.2 1.0
CE1 B:HIS481 3.0 14.3 1.0
HB2 B:HIS481 3.0 13.2 1.0
CE1 B:HIS452 3.0 9.2 1.0
CD2 B:HIS452 3.1 8.6 1.0
CG B:HIS481 3.1 11.2 1.0
HE1 B:HIS481 3.1 17.2 1.0
HB3 B:CYS446 3.1 9.5 1.0
CB B:CYS446 3.1 7.9 1.0
HE1 B:HIS452 3.2 11.0 1.0
HB3 B:CYS478 3.2 11.4 1.0
H B:CYS478 3.2 9.7 1.0
HB2 B:CYS446 3.3 9.5 1.0
HD2 B:HIS452 3.3 10.4 1.0
CB B:CYS478 3.4 9.5 1.0
HB3 B:HIS448 3.4 15.6 1.0
CB B:HIS481 3.5 11.0 1.0
HB2 B:HIS448 3.8 15.6 1.0
N B:CYS478 3.9 8.1 1.0
CB B:HIS448 4.1 13.0 1.0
HB3 B:HIS481 4.1 13.2 1.0
HB2 B:CYS478 4.1 11.4 1.0
NE2 B:HIS481 4.1 17.2 1.0
H B:HIS481 4.1 14.1 1.0
ND1 B:HIS452 4.1 8.9 1.0
CA B:CYS478 4.2 9.4 1.0
CD2 B:HIS481 4.2 15.2 1.0
CG B:HIS452 4.2 8.2 1.0
H B:HIS448 4.3 11.3 1.0
HB2 B:GLU480 4.4 10.4 0.5
N B:HIS481 4.5 11.8 1.0
CA B:CYS446 4.6 7.3 1.0
HG13 B:VAL454 4.7 14.2 1.0
CA B:HIS481 4.7 12.4 1.0
HA B:TYR477 4.7 9.6 1.0
C B:CYS478 4.8 9.5 1.0
HG12 B:VAL454 4.8 14.2 1.0
O B:CYS478 4.8 10.1 1.0
CG B:HIS448 4.9 16.1 1.0
HD1 B:HIS452 4.9 10.7 1.0
HA B:CYS446 4.9 8.7 1.0

Reference:

A.G.W.Matthews, A.J.Kuo, S.Ramon-Maiques, S.Han, K.S.Champagne, D.Ivanov, M.Gallardo, D.Carney, P.Cheung, D.N.Ciccone, K.L.Walter, P.J.Utz, Y.Shi, T.G.Kutateladze, W.Yang, O.Gozani, M.A.Oettinger. RAG2 Phd Finger Couples Histone H3 Lysine 4 Trimethylation with V(D)J Recombination. Nature V. 450 1106 2007.
ISSN: ISSN 0028-0836
PubMed: 18033247
DOI: 10.1038/NATURE06431
Page generated: Wed Dec 16 03:54:37 2020

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