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Zinc in PDB 2v83: Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide

Protein crystallography data

The structure of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide, PDB code: 2v83 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) 30.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.783, 46.835, 56.963, 90.00, 101.46, 90.00
R / Rfree (%) 19.6 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide (pdb code 2v83). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide, PDB code: 2v83:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2v83

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Zinc binding site 1 out of 6 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1486

b:12.9
occ:1.00
ND1 A:HIS455 2.1 11.1 1.0
SG A:CYS419 2.3 10.8 1.0
SG A:CYS458 2.3 9.7 1.0
SG A:CYS423 2.4 11.8 1.0
CG A:HIS455 3.0 11.3 1.0
CE1 A:HIS455 3.1 11.8 1.0
CB A:HIS455 3.3 11.8 1.0
CB A:CYS423 3.3 14.8 1.0
CB A:CYS458 3.4 7.3 1.0
CB A:CYS419 3.5 9.9 1.0
CG2 A:VAL425 3.8 20.7 1.0
CA A:CYS423 3.8 14.4 1.0
N A:CYS419 3.9 12.2 1.0
CB A:VAL425 4.0 20.4 1.0
N A:HIS455 4.1 9.8 1.0
CD2 A:HIS455 4.2 11.1 1.0
NE2 A:HIS455 4.2 12.7 1.0
N A:VAL425 4.2 19.2 1.0
CA A:CYS419 4.2 10.4 1.0
CA A:HIS455 4.3 10.5 1.0
N A:ASP424 4.3 19.2 1.0
C A:CYS423 4.4 17.9 1.0
CA A:VAL425 4.7 19.5 1.0
CA A:CYS458 4.8 6.9 1.0
O A:HIS455 4.8 11.8 1.0
O A:ILE417 4.8 16.9 1.0
N A:CYS420 4.9 9.8 1.0
C A:CYS419 4.9 9.9 1.0
SG A:CYS420 4.9 13.8 1.0

Zinc binding site 2 out of 6 in 2v83

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Zinc binding site 2 out of 6 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1487

b:16.6
occ:1.00
NE2 A:HIS452 2.0 7.3 1.0
ND1 A:HIS481 2.1 22.4 1.0
SG A:CYS446 2.2 14.0 1.0
SG A:CYS478 2.3 15.8 1.0
CE1 A:HIS452 2.8 5.8 1.0
CE1 A:HIS481 2.9 22.0 1.0
CG A:HIS481 3.0 22.6 1.0
CD2 A:HIS452 3.1 7.6 1.0
CB A:CYS446 3.2 12.4 1.0
CB A:CYS478 3.4 10.8 1.0
CB A:HIS481 3.5 22.7 1.0
N A:CYS478 3.9 13.2 1.0
NE2 A:HIS481 3.9 20.9 1.0
ND1 A:HIS452 4.0 7.1 1.0
CD2 A:HIS481 4.0 21.8 1.0
CB A:HIS448 4.1 19.4 1.0
CG A:HIS452 4.1 8.9 1.0
CA A:CYS478 4.2 12.3 1.0
N A:HIS481 4.5 23.2 1.0
CA A:CYS446 4.6 12.6 1.0
CA A:HIS481 4.7 24.0 1.0
O A:CYS478 4.8 11.3 1.0
C A:CYS478 4.8 12.7 1.0
CG A:HIS448 4.9 20.9 1.0
C A:TYR477 5.0 13.4 1.0

Zinc binding site 3 out of 6 in 2v83

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Zinc binding site 3 out of 6 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1488

b:15.8
occ:1.00
ND1 B:HIS455 2.0 12.5 1.0
SG B:CYS458 2.3 15.1 1.0
SG B:CYS423 2.3 24.0 1.0
SG B:CYS419 2.3 18.8 1.0
CE1 B:HIS455 2.8 11.3 1.0
CG B:HIS455 3.1 11.9 1.0
CB B:CYS423 3.3 25.5 1.0
CB B:CYS419 3.4 19.2 1.0
CB B:CYS458 3.4 13.5 1.0
CB B:HIS455 3.5 10.5 1.0
CA B:CYS423 3.8 26.2 1.0
CG2 B:VAL425 3.8 33.4 1.0
N B:CYS419 3.9 17.9 1.0
NE2 B:HIS455 4.0 14.8 1.0
CD2 B:HIS455 4.1 10.4 1.0
N B:HIS455 4.2 11.5 1.0
CB B:VAL425 4.2 32.4 1.0
CA B:CYS419 4.2 18.5 1.0
N B:ASP424 4.3 32.3 1.0
N B:VAL425 4.4 33.4 1.0
C B:CYS423 4.4 28.9 1.0
CA B:HIS455 4.5 10.8 1.0
N B:CYS420 4.7 21.1 1.0
CA B:CYS458 4.7 14.1 1.0
O B:ILE417 4.8 17.6 1.0
C B:CYS419 4.8 19.2 1.0
CA B:VAL425 4.9 32.0 1.0
SG B:CYS420 5.0 24.8 1.0

Zinc binding site 4 out of 6 in 2v83

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Zinc binding site 4 out of 6 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1489

b:16.1
occ:1.00
NE2 B:HIS452 2.0 8.0 1.0
ND1 B:HIS481 2.0 16.8 1.0
SG B:CYS446 2.3 11.1 1.0
SG B:CYS478 2.3 13.0 1.0
CE1 B:HIS481 2.8 16.2 1.0
CE1 B:HIS452 2.8 8.1 1.0
CD2 B:HIS452 3.1 7.5 1.0
CB B:CYS446 3.1 13.0 1.0
CG B:HIS481 3.2 15.7 1.0
CB B:CYS478 3.4 15.8 1.0
CB B:HIS481 3.7 15.5 1.0
N B:CYS478 3.8 16.7 1.0
NE2 B:HIS481 4.0 17.9 1.0
ND1 B:HIS452 4.0 8.5 1.0
CB B:HIS448 4.1 14.2 1.0
CA B:CYS478 4.2 17.8 1.0
CG B:HIS452 4.2 7.5 1.0
CD2 B:HIS481 4.2 15.1 1.0
N B:HIS481 4.6 16.3 1.0
CA B:CYS446 4.6 14.2 1.0
CG B:HIS448 4.8 16.6 1.0
CA B:HIS481 4.8 17.0 1.0
C B:CYS478 4.9 19.4 1.0
O B:CYS478 4.9 21.0 1.0
C B:TYR477 5.0 15.8 1.0

Zinc binding site 5 out of 6 in 2v83

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Zinc binding site 5 out of 6 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1484

b:41.9
occ:1.00
ND1 C:HIS455 2.0 40.4 1.0
SG C:CYS458 2.2 42.9 1.0
SG C:CYS419 2.4 39.4 1.0
SG C:CYS423 2.7 47.8 1.0
CG C:HIS455 2.9 40.4 1.0
CE1 C:HIS455 3.0 39.8 1.0
CB C:HIS455 3.2 41.7 1.0
CB C:CYS458 3.3 43.3 1.0
CB C:CYS423 3.6 48.0 1.0
CB C:CYS419 3.6 43.8 1.0
CA C:CYS423 3.7 47.3 1.0
N C:CYS419 3.9 45.2 1.0
CG2 C:VAL425 4.0 46.5 1.0
CD2 C:HIS455 4.1 39.5 1.0
NE2 C:HIS455 4.1 39.5 1.0
N C:HIS455 4.2 44.7 1.0
N C:ASP424 4.2 49.3 1.0
CA C:CYS419 4.3 44.4 1.0
CA C:HIS455 4.3 43.0 1.0
C C:CYS423 4.5 48.0 1.0
CB C:VAL425 4.5 46.7 1.0
SG C:CYS420 4.6 48.3 1.0
N C:VAL425 4.6 48.6 1.0
N C:CYS420 4.6 45.6 1.0
CA C:CYS458 4.7 43.7 1.0
O C:ILE417 4.8 44.0 1.0
N C:CYS423 4.8 47.0 1.0
C C:CYS419 4.9 44.9 1.0
C C:THR418 5.0 45.0 1.0
N C:CYS458 5.0 44.5 1.0

Zinc binding site 6 out of 6 in 2v83

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Zinc binding site 6 out of 6 in the Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of RAG2-Phd Finger in Complex with H3K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1485

b:57.9
occ:1.00
NE2 C:HIS452 2.1 60.8 1.0
SG C:CYS446 2.2 56.7 1.0
ND1 C:HIS481 2.2 79.5 1.0
SG C:CYS478 2.4 75.0 1.0
CE1 C:HIS481 2.7 79.1 1.0
CB C:CYS446 2.9 60.6 1.0
CE1 C:HIS452 3.0 60.3 1.0
CD2 C:HIS452 3.1 60.8 1.0
CG C:HIS481 3.2 79.6 1.0
CB C:CYS478 3.4 77.2 1.0
NE2 C:HIS481 3.7 78.9 1.0
N C:CYS478 3.7 77.9 1.0
CB C:HIS481 3.8 79.9 1.0
CD2 C:HIS481 4.0 79.1 1.0
CA C:CYS478 4.1 77.3 1.0
ND1 C:HIS452 4.1 60.9 1.0
CB C:HIS448 4.2 69.9 1.0
CG C:HIS452 4.2 60.4 1.0
CA C:CYS446 4.3 61.9 1.0
N C:HIS481 4.7 80.8 1.0
C C:TYR477 4.8 78.1 1.0
C C:CYS478 4.8 77.4 1.0
C C:CYS446 4.8 63.8 1.0
O C:CYS478 4.9 76.9 1.0
CG C:HIS448 4.9 71.0 1.0
CA C:HIS481 5.0 80.2 1.0

Reference:

S.Ramon-Maiques, A.J.Kuo, D.Carney, A.G.W.Matthews, M.A.Oettinger, O.Gozani, W.Yang. The Plant Homeodomain Finger of RAG2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2. Proc.Natl.Acad.Sci.Usa V. 104 18993 2007.
ISSN: ISSN 0027-8424
PubMed: 18025461
DOI: 10.1073/PNAS.0709170104
Page generated: Sat Sep 26 04:00:52 2020
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