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Zinc in PDB 2puy: Crystal Structure of the BHC80 Phd Finger

Protein crystallography data

The structure of Crystal Structure of the BHC80 Phd Finger, PDB code: 2puy was solved by J.R.Horton, X.Cheng, R.E.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.511, 25.386, 62.282, 90.00, 96.93, 90.00
R / Rfree (%) 20.6 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the BHC80 Phd Finger (pdb code 2puy). 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 the BHC80 Phd Finger, PDB code: 2puy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2puy

Go back to Zinc Binding Sites List in 2puy
Zinc binding site 1 out of 4 in the Crystal Structure of the BHC80 Phd Finger


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 the BHC80 Phd Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn355

b:9.3
occ:1.00
ND1 A:HIS511 2.1 7.0 1.0
SG A:CYS514 2.3 10.3 1.0
SG A:CYS494 2.3 9.3 1.0
SG A:CYS491 2.4 8.2 1.0
CE1 A:HIS511 3.0 8.3 1.0
CB A:CYS491 3.1 7.3 1.0
CG A:HIS511 3.2 6.5 1.0
CB A:CYS494 3.4 10.2 1.0
CB A:CYS514 3.4 9.2 1.0
CB A:HIS511 3.5 8.4 1.0
N A:CYS494 3.7 10.7 1.0
CA A:CYS494 4.1 10.8 1.0
N A:HIS511 4.2 6.7 1.0
NE2 A:HIS511 4.2 8.0 1.0
CD2 A:HIS511 4.3 8.8 1.0
CA A:HIS511 4.4 7.7 1.0
CB A:VAL493 4.5 10.4 1.0
CA A:CYS491 4.5 8.4 1.0
CA A:CYS514 4.8 11.3 1.0
C A:VAL493 4.8 11.2 1.0
C A:CYS494 4.8 11.1 1.0
N A:ARG495 4.9 9.9 1.0
N A:VAL493 5.0 10.8 1.0
CA A:VAL493 5.0 11.2 1.0

Zinc binding site 2 out of 4 in 2puy

Go back to Zinc Binding Sites List in 2puy
Zinc binding site 2 out of 4 in the Crystal Structure of the BHC80 Phd Finger


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 the BHC80 Phd Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn356

b:12.2
occ:1.00
SG A:CYS532 2.3 11.9 1.0
SG A:CYS503 2.3 11.6 1.0
SG A:CYS506 2.4 11.5 1.0
SG A:CYS529 2.4 10.8 1.0
CB A:CYS506 3.2 13.8 1.0
CB A:CYS503 3.2 9.4 1.0
CB A:CYS532 3.3 13.8 1.0
CB A:CYS529 3.4 11.6 1.0
N A:CYS506 3.8 13.9 1.0
N A:CYS529 4.0 13.2 1.0
OG1 A:THR505 4.0 15.7 1.0
N A:CYS532 4.0 13.3 1.0
CA A:CYS506 4.0 13.2 1.0
CA A:CYS529 4.2 12.1 1.0
CA A:CYS532 4.2 14.2 1.0
O A:HOH22 4.4 20.4 1.0
C A:THR505 4.5 14.5 1.0
C A:CYS506 4.6 13.8 1.0
O A:CYS529 4.6 12.2 1.0
C A:CYS529 4.7 12.6 1.0
CA A:CYS503 4.7 10.4 1.0
O A:CYS506 4.7 14.2 1.0
CB A:ARG508 4.7 10.6 1.0
N A:THR505 4.9 14.0 1.0
CD A:ARG508 4.9 14.1 1.0
CA A:THR505 5.0 14.7 1.0

Zinc binding site 3 out of 4 in 2puy

Go back to Zinc Binding Sites List in 2puy
Zinc binding site 3 out of 4 in the Crystal Structure of the BHC80 Phd Finger


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 the BHC80 Phd Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn357

b:8.6
occ:1.00
ND1 B:HIS511 2.1 7.5 1.0
SG B:CYS491 2.3 7.5 1.0
SG B:CYS514 2.3 10.5 1.0
SG B:CYS494 2.3 8.2 1.0
CB B:CYS491 3.0 7.8 1.0
CE1 B:HIS511 3.0 7.1 1.0
CG B:HIS511 3.1 7.8 1.0
CB B:CYS514 3.3 11.9 1.0
CB B:CYS494 3.4 8.6 1.0
CB B:HIS511 3.5 7.1 1.0
N B:CYS494 3.8 9.3 1.0
N B:HIS511 4.1 6.9 1.0
CA B:CYS494 4.2 9.6 1.0
NE2 B:HIS511 4.2 8.4 1.0
CD2 B:HIS511 4.2 8.2 1.0
CA B:HIS511 4.4 7.1 1.0
CA B:CYS491 4.5 7.2 1.0
CB B:VAL493 4.6 10.2 1.0
CA B:CYS514 4.7 11.2 1.0
C B:VAL493 4.8 10.6 1.0
C B:CYS494 4.9 11.1 1.0
N B:VAL493 5.0 9.8 1.0
N B:ARG495 5.0 10.7 1.0

Zinc binding site 4 out of 4 in 2puy

Go back to Zinc Binding Sites List in 2puy
Zinc binding site 4 out of 4 in the Crystal Structure of the BHC80 Phd Finger


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 the BHC80 Phd Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn358

b:9.1
occ:1.00
SG B:CYS532 2.3 10.0 1.0
SG B:CYS503 2.3 8.2 1.0
SG B:CYS506 2.3 9.9 1.0
SG B:CYS529 2.4 9.6 1.0
CB B:CYS503 3.3 9.7 1.0
CB B:CYS506 3.3 8.7 1.0
CB B:CYS532 3.3 10.1 1.0
CB B:CYS529 3.4 8.3 1.0
N B:CYS506 3.8 9.8 1.0
OG1 B:THR505 3.9 12.1 1.0
N B:CYS529 4.0 9.8 1.0
N B:CYS532 4.0 12.0 1.0
CA B:CYS506 4.0 9.7 1.0
CA B:CYS529 4.2 9.4 1.0
CA B:CYS532 4.2 11.7 1.0
C B:THR505 4.4 10.8 1.0
NH1 B:ARG508 4.4 16.4 1.0
C B:CYS506 4.6 9.4 1.0
O B:CYS529 4.7 10.7 1.0
CA B:CYS503 4.7 8.7 1.0
C B:CYS529 4.7 10.5 1.0
CB B:ARG508 4.7 7.6 1.0
O B:CYS506 4.8 10.7 1.0
N B:THR505 4.8 10.8 1.0
CA B:THR505 4.9 11.5 1.0
O B:THR505 4.9 11.2 1.0
CB B:THR505 4.9 11.6 1.0
CD B:ARG508 4.9 12.8 1.0

Reference:

F.Lan, R.E.Collins, R.De Cegli, R.Alpatov, J.R.Horton, X.Shi, O.Gozani, X.Cheng, Y.Shi. Recognition of Unmethylated Histone H3 Lysine 4 Links BHC80 to LSD1-Mediated Gene Repression. Nature V. 448 718 2007.
ISSN: ISSN 0028-0836
PubMed: 17687328
DOI: 10.1038/NATURE06034
Page generated: Wed Dec 16 03:49:11 2020

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