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Zinc in PDB 4rn5: B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site

Protein crystallography data

The structure of B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site, PDB code: 4rn5 was solved by C.K.Allerston, T.S.Yelland, A.Jarvis, K.Jenkins, N.Winfield, L.Cheng, H.Jia, I.Zachary, D.L.Selwood, S.Djordjevic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.54 / 1.73
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.839, 62.839, 87.918, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site (pdb code 4rn5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site, PDB code: 4rn5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4rn5

Go back to Zinc Binding Sites List in 4rn5
Zinc binding site 1 out of 2 in the B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:19.1
occ:1.00
NE2 A:HIS287 2.1 15.7 1.0
O A:HOH685 2.3 16.6 1.0
CE1 A:HIS287 3.1 20.6 1.0
CD2 A:HIS287 3.1 17.6 1.0
O A:HOH679 4.1 24.6 1.0
ND1 A:HIS287 4.2 20.3 1.0
O A:GLU285 4.2 16.4 1.0
O A:HOH686 4.2 25.2 1.0
CG A:HIS287 4.2 15.6 1.0
O A:HOH758 4.3 26.7 1.0
O A:HOH732 4.6 37.6 1.0

Zinc binding site 2 out of 2 in 4rn5

Go back to Zinc Binding Sites List in 4rn5
Zinc binding site 2 out of 2 in the B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of B1 Domain of Human Neuropilin-1 with Acetate Ion in A Ligand-Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:47.8
occ:1.00
O A:HOH755 2.4 24.6 1.0
O A:HOH756 2.4 34.2 1.0
OD2 A:ASP289 2.6 21.9 1.0
O A:HOH757 2.6 36.5 1.0
O A:HOH759 2.9 38.3 1.0
OD1 A:ASP289 3.2 20.6 1.0
CG A:ASP289 3.3 17.9 1.0
O A:HOH758 3.8 26.7 1.0
O A:HOH728 4.1 29.7 1.0
O A:HOH716 4.4 31.4 1.0
O A:HOH633 4.6 16.8 1.0
CB A:ASP289 4.7 14.8 1.0
CB A:HIS287 4.8 10.1 1.0
CD2 A:HIS287 4.9 17.6 1.0
O A:HOH742 4.9 34.9 1.0
O A:HOH686 5.0 25.2 1.0
CG A:HIS287 5.0 15.6 1.0

Reference:

C.K.Allerston, T.S.Yelland, A.Jarvis, K.Jenkins, N.Winfield, L.Cheng, H.Jia, I.Zachary, D.L.Selwood, S.Djordjevic. Conserved Water Molecules in A Ligand-Binding Site of Neuropilin-1 To Be Published.
Page generated: Wed Dec 16 05:46:06 2020

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