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Zinc in PDB 2h1n: 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique

Protein crystallography data

The structure of 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique, PDB code: 2h1n was solved by C.J.Gerdts, V.Tereshko, I.Dementieva, F.Collart, A.Joachimiak, A.Kossiakoff, R.F.Ismagilov, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.987, 119.987, 249.747, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique (pdb code 2h1n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique, PDB code: 2h1n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2h1n

Go back to Zinc Binding Sites List in 2h1n
Zinc binding site 1 out of 2 in the 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:60.3
occ:1.00
NE2 A:HIS360 2.1 60.4 1.0
NE2 A:HIS356 2.1 61.4 1.0
OE2 A:GLU384 2.3 64.8 1.0
OE1 A:GLU384 2.6 65.3 1.0
O A:HOH602 2.6 33.7 1.0
CD A:GLU384 2.8 65.0 1.0
CD2 A:HIS360 3.1 60.9 1.0
CE1 A:HIS356 3.1 61.0 1.0
CD2 A:HIS356 3.1 61.4 1.0
CE1 A:HIS360 3.1 60.2 1.0
OG A:SER387 3.5 70.9 1.0
CE2 A:TYR490 3.7 65.2 1.0
OH A:TYR490 3.7 65.7 1.0
CZ A:TYR490 4.2 65.3 1.0
CB A:SER387 4.2 71.6 1.0
ND1 A:HIS356 4.2 61.7 1.0
ND1 A:HIS360 4.2 59.9 1.0
OH A:TYR486 4.2 68.4 1.0
CG A:HIS360 4.2 60.8 1.0
CG A:HIS356 4.3 62.0 1.0
CG A:GLU384 4.3 64.7 1.0
CD2 A:TYR490 4.8 64.8 1.0

Zinc binding site 2 out of 2 in 2h1n

Go back to Zinc Binding Sites List in 2h1n
Zinc binding site 2 out of 2 in the 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 3.0 A X-Ray Structure of Putative Oligoendopeptidase F: Crystals Grown By Vapor Diffusion Technique within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:66.6
occ:1.00
NE2 B:HIS360 2.1 59.1 1.0
NE2 B:HIS356 2.1 60.6 1.0
OE2 B:GLU384 2.3 64.0 1.0
O B:HOH702 2.7 39.1 1.0
OE1 B:GLU384 2.7 65.7 1.0
CD B:GLU384 2.9 64.9 1.0
CD2 B:HIS356 3.1 60.9 1.0
CE1 B:HIS360 3.1 59.3 1.0
CE1 B:HIS356 3.1 60.2 1.0
CD2 B:HIS360 3.1 59.9 1.0
OG B:SER387 3.6 71.4 1.0
CE2 B:TYR490 3.8 65.5 1.0
OH B:TYR490 3.8 65.5 1.0
OE2 B:GLU357 4.1 69.6 1.0
OH B:TYR486 4.2 67.5 1.0
CB B:SER387 4.2 71.7 1.0
ND1 B:HIS360 4.2 59.6 1.0
ND1 B:HIS356 4.2 60.6 1.0
CG B:HIS356 4.2 61.4 1.0
CG B:HIS360 4.2 60.3 1.0
CZ B:TYR490 4.3 65.3 1.0
CG B:GLU384 4.4 65.1 1.0
CD2 B:TYR490 4.8 65.2 1.0
CD B:GLU357 4.9 68.8 1.0
OE1 B:GLU357 5.0 70.8 1.0

Reference:

C.J.Gerdts, V.Tereshko, M.K.Yadav, I.Dementieva, F.Collart, A.Joachimiak, R.C.Stevens, P.Kuhn, A.Kossiakoff, R.F.Ismagilov. Time-Controlled Microfluidic Seeding in Nl-Volume Droplets to Separate Nucleation and Growth Stages of Protein Crystallization. Angew.Chem.Int.Ed.Engl. V. 45 8156 2006.
ISSN: ISSN 1433-7851
PubMed: 17099920
DOI: 10.1002/ANIE.200602946
Page generated: Sat Sep 26 02:12:46 2020
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