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Zinc in PDB 1bnl: Zinc Dependent Dimers Observed in Crystals of Human Endostatin

Protein crystallography data

The structure of Zinc Dependent Dimers Observed in Crystals of Human Endostatin, PDB code: 1bnl was solved by Y.-H.Ding, K.Javaherian, K.-M.Lo, R.Chopra, T.Boehm, J.Lanciotti, B.A.Harris, Y.Li, R.Shapiro, E.Hohenester, R.Timpl, J.Folkman, D.C.Wiley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.713, 74.266, 137.805, 90.00, 102.55, 90.00
R / Rfree (%) 24 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Zinc Dependent Dimers Observed in Crystals of Human Endostatin (pdb code 1bnl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zinc Dependent Dimers Observed in Crystals of Human Endostatin, PDB code: 1bnl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1bnl

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Zinc binding site 1 out of 4 in the Zinc Dependent Dimers Observed in Crystals of Human Endostatin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Dependent Dimers Observed in Crystals of Human Endostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn179

b:10.0
occ:1.00
ND1 A:HIS1 2.0 33.8 1.0
NE2 A:HIS3 2.0 14.4 1.0
OD1 A:ASP76 2.1 13.7 1.0
NE2 A:HIS11 2.3 10.0 1.0
CE1 A:HIS1 2.5 34.0 1.0
CE1 A:HIS3 2.9 15.4 1.0
CE1 A:HIS11 2.9 11.7 1.0
CD2 A:HIS3 3.1 14.6 1.0
CG A:HIS1 3.3 33.6 1.0
CG A:ASP76 3.4 14.2 1.0
CD2 A:HIS11 3.4 10.0 1.0
NE2 A:HIS1 3.7 32.3 1.0
CB A:HIS1 4.0 37.5 1.0
ND1 A:HIS3 4.1 16.2 1.0
OD2 A:ASP76 4.1 14.8 1.0
CD2 A:HIS1 4.1 33.8 1.0
ND1 A:HIS11 4.1 10.1 1.0
CG A:HIS3 4.2 13.5 1.0
CG A:HIS11 4.4 10.0 1.0
CB A:ASP76 4.4 11.8 1.0
CA A:ASP76 4.7 14.9 1.0
CA A:HIS1 4.7 36.5 1.0
CG1 A:VAL9 4.7 10.0 1.0
N A:ASP76 5.0 15.7 1.0

Zinc binding site 2 out of 4 in 1bnl

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Zinc binding site 2 out of 4 in the Zinc Dependent Dimers Observed in Crystals of Human Endostatin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Dependent Dimers Observed in Crystals of Human Endostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn179

b:10.0
occ:1.00
ND1 B:HIS1 2.0 33.8 1.0
NE2 B:HIS3 2.0 14.4 1.0
OD1 B:ASP76 2.1 13.7 1.0
NE2 B:HIS11 2.3 10.0 1.0
CE1 B:HIS1 2.5 34.0 1.0
CE1 B:HIS3 2.9 15.4 1.0
CE1 B:HIS11 2.9 11.7 1.0
CD2 B:HIS3 3.1 14.6 1.0
CG B:HIS1 3.3 33.6 1.0
CG B:ASP76 3.4 14.2 1.0
CD2 B:HIS11 3.4 10.0 1.0
NE2 B:HIS1 3.7 32.3 1.0
CB B:HIS1 4.0 37.5 1.0
ND1 B:HIS3 4.1 16.2 1.0
OD2 B:ASP76 4.1 14.8 1.0
CD2 B:HIS1 4.1 33.8 1.0
ND1 B:HIS11 4.1 10.1 1.0
CG B:HIS3 4.2 13.5 1.0
CG B:HIS11 4.4 10.0 1.0
CB B:ASP76 4.4 11.8 1.0
CA B:ASP76 4.7 14.9 1.0
CA B:HIS1 4.7 36.5 1.0
CG1 B:VAL9 4.7 10.0 1.0
N B:ASP76 5.0 15.7 1.0

Zinc binding site 3 out of 4 in 1bnl

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Zinc binding site 3 out of 4 in the Zinc Dependent Dimers Observed in Crystals of Human Endostatin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Dependent Dimers Observed in Crystals of Human Endostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn179

b:10.0
occ:1.00
ND1 C:HIS1 2.0 33.8 1.0
NE2 C:HIS3 2.0 14.4 1.0
OD1 C:ASP76 2.1 13.7 1.0
NE2 C:HIS11 2.3 10.0 1.0
CE1 C:HIS1 2.5 34.0 1.0
CE1 C:HIS3 2.9 15.4 1.0
CE1 C:HIS11 2.9 11.7 1.0
CD2 C:HIS3 3.1 14.6 1.0
CG C:HIS1 3.3 33.6 1.0
CG C:ASP76 3.4 14.2 1.0
CD2 C:HIS11 3.4 10.0 1.0
NE2 C:HIS1 3.7 32.3 1.0
CB C:HIS1 4.0 37.5 1.0
ND1 C:HIS3 4.1 16.2 1.0
OD2 C:ASP76 4.1 14.8 1.0
CD2 C:HIS1 4.1 33.8 1.0
ND1 C:HIS11 4.1 10.1 1.0
CG C:HIS3 4.2 13.5 1.0
CG C:HIS11 4.4 10.0 1.0
CB C:ASP76 4.4 11.8 1.0
CA C:ASP76 4.7 14.9 1.0
CA C:HIS1 4.7 36.5 1.0
CG1 C:VAL9 4.7 10.0 1.0
N C:ASP76 5.0 15.7 1.0

Zinc binding site 4 out of 4 in 1bnl

Go back to Zinc Binding Sites List in 1bnl
Zinc binding site 4 out of 4 in the Zinc Dependent Dimers Observed in Crystals of Human Endostatin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Dependent Dimers Observed in Crystals of Human Endostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn179

b:10.0
occ:1.00
ND1 D:HIS1 2.0 33.8 1.0
NE2 D:HIS3 2.0 14.4 1.0
OD1 D:ASP76 2.1 13.7 1.0
NE2 D:HIS11 2.3 10.0 1.0
CE1 D:HIS1 2.5 34.0 1.0
CE1 D:HIS3 2.9 15.4 1.0
CE1 D:HIS11 2.9 11.7 1.0
CD2 D:HIS3 3.1 14.6 1.0
CG D:HIS1 3.3 33.6 1.0
CG D:ASP76 3.4 14.2 1.0
CD2 D:HIS11 3.4 10.0 1.0
NE2 D:HIS1 3.7 32.3 1.0
CB D:HIS1 4.0 37.5 1.0
ND1 D:HIS3 4.1 16.2 1.0
OD2 D:ASP76 4.1 14.8 1.0
CD2 D:HIS1 4.1 33.8 1.0
ND1 D:HIS11 4.1 10.1 1.0
CG D:HIS3 4.2 13.5 1.0
CG D:HIS11 4.4 10.0 1.0
CB D:ASP76 4.4 11.8 1.0
CA D:ASP76 4.7 14.9 1.0
CA D:HIS1 4.7 36.5 1.0
CG1 D:VAL9 4.7 10.0 1.0
N D:ASP76 5.0 15.7 1.0

Reference:

Y.H.Ding, K.Javaherian, K.M.Lo, R.Chopra, T.Boehm, J.Lanciotti, B.A.Harris, Y.Li, R.Shapiro, E.Hohenester, R.Timpl, J.Folkman, D.C.Wiley. Zinc-Dependent Dimers Observed in Crystals of Human Endostatin. Proc.Natl.Acad.Sci.Usa V. 95 10443 1998.
ISSN: ISSN 0027-8424
PubMed: 9724722
DOI: 10.1073/PNAS.95.18.10443
Page generated: Wed Dec 16 02:45:52 2020

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