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Zinc in PDB 1btg: Crystal Structure of Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound

Protein crystallography data

The structure of Crystal Structure of Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound, PDB code: 1btg was solved by D.R.Holland, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.800, 93.900, 58.900, 90.00, 123.10, 90.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound (pdb code 1btg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound, PDB code: 1btg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1btg

Go back to Zinc Binding Sites List in 1btg
Zinc binding site 1 out of 3 in the Crystal Structure of Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound


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 Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:42.2
occ:1.00
O B:HOH962 1.9 41.6 1.0
O B:HOH961 1.9 42.4 1.0
OD1 B:ASP105 2.0 19.9 1.0
NE2 B:HIS84 2.1 30.4 1.0
CE1 B:HIS84 3.0 28.5 1.0
CG B:ASP105 3.1 20.3 1.0
CD2 B:HIS84 3.1 30.0 1.0
OD2 B:ASP105 3.3 22.0 1.0
ND1 B:HIS84 4.1 27.9 1.0
CG B:HIS84 4.2 27.4 1.0
OG1 B:THR82 4.3 21.3 1.0
CB B:ASP105 4.4 14.8 1.0
NH2 B:ARG103 4.5 80.0 1.0
CA B:ASP105 4.8 14.5 1.0
CB B:THR82 5.0 15.6 1.0

Zinc binding site 2 out of 3 in 1btg

Go back to Zinc Binding Sites List in 1btg
Zinc binding site 2 out of 3 in the Crystal Structure of Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound


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 Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn900

b:36.9
occ:1.00
O C:HOH959 1.8 33.4 1.0
O C:HOH958 2.1 36.1 1.0
NE2 C:HIS84 2.1 28.1 1.0
OD1 C:ASP105 2.4 20.6 1.0
CE1 C:HIS84 3.0 28.2 1.0
CD2 C:HIS84 3.1 26.7 1.0
CG C:ASP105 3.5 23.3 1.0
ZN C:ZN901 3.5 30.7 1.0
OD2 C:ASP105 3.8 25.1 1.0
ND1 C:HIS84 4.1 29.4 1.0
CG C:HIS84 4.2 26.6 1.0
O C:HOH960 4.7 38.7 1.0
CB C:ASP105 4.7 6.2 1.0
CG2 C:THR82 4.7 18.8 1.0
CA C:ASP105 4.7 7.4 1.0
O C:HOH950 4.8 19.0 1.0
N C:ASP105 4.8 13.6 1.0

Zinc binding site 3 out of 3 in 1btg

Go back to Zinc Binding Sites List in 1btg
Zinc binding site 3 out of 3 in the Crystal Structure of Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound


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 Beta Nerve Growth Factor at 2.5 A Resolution in C2 Space Group with Zn Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:30.7
occ:1.00
OD2 C:ASP105 1.9 25.1 1.0
O C:HOH960 2.3 38.7 1.0
O C:HOH959 2.4 33.4 1.0
CG C:ASP105 2.7 23.3 1.0
OD1 C:ASP105 3.1 20.6 1.0
ZN C:ZN900 3.5 36.9 1.0
O C:HOH958 3.8 36.1 1.0
CE C:LYS57 3.9 11.9 1.0
CB C:ASP105 4.1 6.2 1.0
NZ C:LYS57 4.2 18.0 1.0
CD C:LYS57 4.4 6.7 1.0
CG2 C:THR82 4.6 18.8 1.0
O C:HOH950 4.7 19.0 1.0
CB C:LYS57 4.9 16.3 1.0

Reference:

D.R.Holland, L.S.Cousens, W.Meng, B.W.Matthews. Nerve Growth Factor in Different Crystal Forms Displays Structural Flexibility and Reveals Zinc Binding Sites. J.Mol.Biol. V. 239 385 1994.
ISSN: ISSN 0022-2836
PubMed: 8201620
DOI: 10.1006/JMBI.1994.1380
Page generated: Wed Dec 16 02:46:03 2020

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