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Zinc in PDB 2v86: Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2AK4ME3 Peptide

Protein crystallography data

The structure of Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2AK4ME3 Peptide, PDB code: 2v86 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 / 2.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 62.905, 66.569, 87.495, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2AK4ME3 Peptide (pdb code 2v86). 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 H3R2ME2AK4ME3 Peptide, PDB code: 2v86:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2v86

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Zinc binding site 1 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2AK4ME3 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 H3R2ME2AK4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1488

b:9.9
occ:1.00
ND1 A:HIS455 2.0 6.0 1.0
SG A:CYS458 2.3 7.7 1.0
SG A:CYS419 2.3 8.2 1.0
SG A:CYS423 2.4 8.4 1.0
CG A:HIS455 2.9 8.3 1.0
CE1 A:HIS455 3.1 7.1 1.0
CB A:HIS455 3.2 8.1 1.0
CB A:CYS458 3.3 7.0 1.0
CB A:CYS423 3.3 12.8 1.0
CB A:CYS419 3.4 8.9 1.0
CA A:CYS423 3.7 14.7 1.0
N A:CYS419 3.9 12.4 1.0
CG2 A:VAL425 4.1 19.8 1.0
CD2 A:HIS455 4.1 7.0 1.0
CB A:VAL425 4.1 20.5 1.0
NE2 A:HIS455 4.2 7.5 1.0
N A:HIS455 4.2 8.0 1.0
CA A:CYS419 4.2 12.1 1.0
N A:ASP424 4.3 20.3 1.0
CA A:HIS455 4.3 7.4 1.0
N A:VAL425 4.3 21.5 1.0
C A:CYS423 4.4 16.8 1.0
CA A:CYS458 4.7 8.2 1.0
N A:CYS420 4.7 12.6 1.0
O A:ILE417 4.7 13.3 1.0
C A:CYS419 4.8 12.5 1.0
CA A:VAL425 4.9 19.8 1.0
SG A:CYS420 4.9 11.0 1.0
N A:CYS423 4.9 14.4 1.0
O A:HIS455 4.9 8.0 1.0

Zinc binding site 2 out of 4 in 2v86

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Zinc binding site 2 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2AK4ME3 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 H3R2ME2AK4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1489

b:11.1
occ:1.00
NE2 A:HIS452 2.1 7.3 1.0
ND1 A:HIS481 2.1 6.4 1.0
SG A:CYS446 2.2 7.6 1.0
SG A:CYS478 2.3 8.1 1.0
CE1 A:HIS481 2.9 8.2 1.0
CD2 A:HIS452 3.1 11.3 1.0
CE1 A:HIS452 3.1 10.3 1.0
CB A:CYS446 3.1 7.7 1.0
CG A:HIS481 3.2 7.2 1.0
CB A:CYS478 3.4 8.8 1.0
CB A:HIS481 3.7 8.5 1.0
N A:CYS478 3.8 7.5 1.0
CB A:HIS448 3.9 8.6 1.0
NE2 A:HIS481 4.1 8.1 1.0
CA A:CYS478 4.1 9.5 1.0
ND1 A:HIS452 4.2 11.9 1.0
CG A:HIS452 4.2 11.4 1.0
CD2 A:HIS481 4.3 5.9 1.0
N A:HIS481 4.6 10.7 1.0
CA A:CYS446 4.6 7.3 1.0
CG A:HIS448 4.7 6.8 1.0
O A:CYS478 4.8 8.0 1.0
C A:CYS478 4.8 8.9 1.0
CA A:HIS481 4.8 10.2 1.0
N A:HIS448 4.9 7.7 1.0
C A:TYR477 5.0 8.8 1.0
C A:CYS446 5.0 8.9 1.0

Zinc binding site 3 out of 4 in 2v86

Go back to Zinc Binding Sites List in 2v86
Zinc binding site 3 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2AK4ME3 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 H3R2ME2AK4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1488

b:9.0
occ:1.00
ND1 B:HIS455 2.1 2.2 1.0
SG B:CYS458 2.3 10.6 1.0
SG B:CYS419 2.3 7.5 1.0
SG B:CYS423 2.4 8.8 1.0
CG B:HIS455 3.0 6.0 1.0
CE1 B:HIS455 3.1 5.0 1.0
CB B:CYS458 3.3 9.4 1.0
CB B:HIS455 3.3 6.0 1.0
CB B:CYS419 3.3 7.8 1.0
CB B:CYS423 3.4 8.4 1.0
CA B:CYS423 3.8 10.8 1.0
N B:CYS419 3.9 11.1 1.0
N B:ASP424 4.1 15.5 1.0
N B:HIS455 4.1 6.5 1.0
CA B:CYS419 4.1 9.5 1.0
NE2 B:HIS455 4.2 4.9 1.0
CD2 B:HIS455 4.2 3.2 1.0
CB B:VAL425 4.2 15.9 1.0
N B:VAL425 4.3 18.9 1.0
CA B:HIS455 4.3 5.9 1.0
C B:CYS423 4.5 12.7 1.0
CG2 B:VAL425 4.6 18.2 1.0
CA B:CYS458 4.7 8.4 1.0
N B:CYS420 4.7 10.4 1.0
O B:ILE417 4.8 11.6 1.0
C B:CYS419 4.8 10.2 1.0
SG B:CYS420 4.9 8.6 1.0
CA B:VAL425 4.9 15.6 1.0
O B:HIS455 5.0 5.0 1.0
N B:CYS423 5.0 9.6 1.0
N B:CYS458 5.0 8.4 1.0

Zinc binding site 4 out of 4 in 2v86

Go back to Zinc Binding Sites List in 2v86
Zinc binding site 4 out of 4 in the Crystal Structure of RAG2-Phd Finger in Complex with H3R2ME2AK4ME3 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 H3R2ME2AK4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1489

b:10.7
occ:1.00
NE2 B:HIS452 2.0 8.5 1.0
ND1 B:HIS481 2.1 6.4 1.0
SG B:CYS446 2.3 7.8 1.0
SG B:CYS478 2.3 8.2 1.0
CE1 B:HIS452 2.9 8.9 1.0
CE1 B:HIS481 2.9 8.2 1.0
CD2 B:HIS452 3.1 6.9 1.0
CB B:CYS446 3.2 7.0 1.0
CG B:HIS481 3.2 7.8 1.0
CB B:CYS478 3.4 10.3 1.0
CB B:HIS481 3.7 7.1 1.0
N B:CYS478 3.8 8.1 1.0
CB B:HIS448 4.0 6.2 1.0
ND1 B:HIS452 4.0 8.9 1.0
NE2 B:HIS481 4.1 8.9 1.0
CA B:CYS478 4.2 9.6 1.0
CG B:HIS452 4.2 9.0 1.0
CD2 B:HIS481 4.3 5.7 1.0
N B:HIS481 4.4 7.5 1.0
CA B:CYS446 4.7 7.6 1.0
CA B:HIS481 4.7 8.1 1.0
C B:CYS478 4.8 9.8 1.0
CG B:HIS448 4.8 6.4 1.0
O B:CYS478 4.8 7.9 1.0
CB B:GLU480 5.0 14.3 1.0
C B:TYR477 5.0 9.1 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: Wed Dec 16 03:54:34 2020

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