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Zinc in PDB 1lrh: Crystal Structure of Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid

Protein crystallography data

The structure of Crystal Structure of Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid, PDB code: 1lrh was solved by E.J.Woo, J.Marshall, J.Bauly, J.-G.Chen, M.Venis, R.M.Napier, R.W.Pickersgill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.583, 82.433, 69.962, 90.00, 94.37, 90.00
R / Rfree (%) 20 / 24

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid (pdb code 1lrh). 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 Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid, PDB code: 1lrh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1lrh

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Zinc binding site 1 out of 4 in the Crystal Structure of Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid


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 Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn180

b:13.4
occ:1.00
NE2 A:HIS106 2.2 7.0 1.0
NE2 A:HIS57 2.3 11.4 1.0
NE2 A:HIS59 2.3 12.1 1.0
O2 A:NLA5190 2.4 20.4 1.0
OE1 A:GLU63 2.4 13.9 1.0
O1 A:NLA5190 2.5 21.2 1.0
C12 A:NLA5190 2.8 22.1 1.0
CE1 A:HIS106 3.0 8.2 1.0
CD2 A:HIS57 3.1 10.5 1.0
CD A:GLU63 3.2 16.2 1.0
CD2 A:HIS106 3.2 10.1 1.0
CD2 A:HIS59 3.3 12.9 1.0
CE1 A:HIS57 3.3 13.6 1.0
OE2 A:GLU63 3.3 18.2 1.0
CE1 A:HIS59 3.3 12.9 1.0
ND1 A:HIS106 4.2 6.1 1.0
C11 A:NLA5190 4.2 23.8 1.0
CG A:HIS57 4.3 8.2 1.0
ND1 A:HIS57 4.3 10.4 1.0
CG A:HIS106 4.3 7.1 1.0
ND1 A:HIS59 4.4 13.4 1.0
CG A:HIS59 4.4 12.9 1.0
C3 A:NLA5190 4.5 26.5 1.0
CG A:GLU63 4.6 12.4 1.0
CZ A:PHE65 4.7 8.1 1.0
CE1 A:PHE65 4.9 9.7 1.0
C2 A:NLA5190 4.9 26.1 1.0

Zinc binding site 2 out of 4 in 1lrh

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Zinc binding site 2 out of 4 in the Crystal Structure of Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid


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 Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn180

b:12.2
occ:1.00
NE2 B:HIS106 2.2 7.0 1.0
NE2 B:HIS59 2.2 11.0 1.0
NE2 B:HIS57 2.3 12.5 1.0
O2 B:NLA6190 2.4 24.4 1.0
O1 B:NLA6190 2.5 22.6 1.0
OE1 B:GLU63 2.5 13.2 1.0
C12 B:NLA6190 2.8 25.5 1.0
CE1 B:HIS106 3.0 7.8 1.0
CD2 B:HIS59 3.1 10.5 1.0
CE1 B:HIS57 3.2 12.0 1.0
CE1 B:HIS59 3.2 12.0 1.0
CD2 B:HIS57 3.2 11.9 1.0
CD2 B:HIS106 3.3 8.6 1.0
CD B:GLU63 3.3 16.6 1.0
OE2 B:GLU63 3.4 17.0 1.0
ND1 B:HIS106 4.2 6.5 1.0
C11 B:NLA6190 4.2 25.6 1.0
CG B:HIS59 4.3 10.3 1.0
ND1 B:HIS59 4.3 8.3 1.0
ND1 B:HIS57 4.3 10.9 1.0
CG B:HIS106 4.3 7.6 1.0
CG B:HIS57 4.3 12.5 1.0
C3 B:NLA6190 4.3 27.8 1.0
CG B:GLU63 4.8 12.1 1.0
C2 B:NLA6190 4.8 26.5 1.0
CZ B:PHE65 4.8 11.2 1.0
CE1 B:PHE65 5.0 10.7 1.0

Zinc binding site 3 out of 4 in 1lrh

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Zinc binding site 3 out of 4 in the Crystal Structure of Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid


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 Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn180

b:14.6
occ:1.00
NE2 C:HIS59 2.2 9.6 1.0
NE2 C:HIS106 2.3 10.2 1.0
OE1 C:GLU63 2.3 12.2 1.0
O1 C:NLA7190 2.3 19.4 1.0
NE2 C:HIS57 2.4 14.5 1.0
O2 C:NLA7190 2.5 21.7 1.0
C12 C:NLA7190 2.7 21.6 1.0
CE1 C:HIS106 3.0 12.4 1.0
CE1 C:HIS59 3.0 12.3 1.0
CD C:GLU63 3.2 13.5 1.0
CD2 C:HIS59 3.2 11.5 1.0
CD2 C:HIS57 3.3 13.7 1.0
CE1 C:HIS57 3.3 14.4 1.0
CD2 C:HIS106 3.4 11.4 1.0
OE2 C:GLU63 3.4 15.1 1.0
C11 C:NLA7190 4.2 20.6 1.0
ND1 C:HIS106 4.2 11.7 1.0
ND1 C:HIS59 4.2 10.2 1.0
CG C:HIS59 4.3 10.8 1.0
CG C:HIS106 4.4 12.8 1.0
C3 C:NLA7190 4.4 18.5 1.0
ND1 C:HIS57 4.4 13.6 1.0
CG C:HIS57 4.5 14.1 1.0
CG C:GLU63 4.6 10.4 1.0
CZ C:PHE65 4.7 10.6 1.0
C2 C:NLA7190 4.8 21.7 1.0
CE1 C:PHE65 4.9 10.2 1.0

Zinc binding site 4 out of 4 in 1lrh

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Zinc binding site 4 out of 4 in the Crystal Structure of Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid


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 Auxin-Binding Protein 1 in Complex with 1- Naphthalene Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn180

b:11.8
occ:1.00
NE2 D:HIS57 2.2 9.6 1.0
NE2 D:HIS106 2.2 8.7 1.0
O2 D:NLA8190 2.3 15.4 1.0
NE2 D:HIS59 2.4 11.1 1.0
OE1 D:GLU63 2.4 13.5 1.0
O1 D:NLA8190 2.4 15.4 1.0
C12 D:NLA8190 2.6 15.8 1.0
CE1 D:HIS106 3.0 10.1 1.0
CE1 D:HIS57 3.0 12.6 1.0
CD2 D:HIS59 3.2 10.9 1.0
CD2 D:HIS106 3.3 9.3 1.0
CD2 D:HIS57 3.3 9.3 1.0
CE1 D:HIS59 3.3 10.6 1.0
CD D:GLU63 3.4 14.2 1.0
OE2 D:GLU63 3.6 16.1 1.0
C11 D:NLA8190 4.1 15.9 1.0
ND1 D:HIS57 4.2 10.2 1.0
ND1 D:HIS106 4.2 9.0 1.0
C3 D:NLA8190 4.3 17.5 1.0
CG D:HIS57 4.3 9.7 1.0
CG D:HIS106 4.3 8.3 1.0
CG D:HIS59 4.3 8.7 1.0
ND1 D:HIS59 4.4 8.6 1.0
CZ D:PHE65 4.6 9.0 1.0
C2 D:NLA8190 4.7 17.4 1.0
CG D:GLU63 4.7 8.2 1.0
CE1 D:PHE65 4.9 10.3 1.0

Reference:

E.J.Woo, J.Marshall, J.Bauly, J.G.Chen, M.Venis, R.M.Napier, R.W.Pickersgill. Crystal Structure of Auxin-Binding Protein 1 in Complex with Auxin. Embo J. V. 21 2877 2002.
ISSN: ISSN 0261-4189
PubMed: 12065401
DOI: 10.1093/EMBOJ/CDF291
Page generated: Fri Sep 25 22:29:29 2020
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