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Zinc in PDB 5dq0: Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site

Protein crystallography data

The structure of Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site, PDB code: 5dq0 was solved by Y.I.Tsai, R.R.Rana, I.Zachary, S.Djordjevic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.13 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 99.390, 105.270, 45.750, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.7

Other elements in 5dq0:

The structure of Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site (pdb code 5dq0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site, PDB code: 5dq0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5dq0

Go back to Zinc Binding Sites List in 5dq0
Zinc binding site 1 out of 3 in the Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:18.6
occ:1.00
OH A:TYR375 1.9 17.2 1.0
ND1 A:HIS399 2.1 23.7 1.0
NE2 A:HIS377 2.1 21.3 1.0
CL A:CL505 2.1 20.6 1.0
CE1 A:HIS399 2.9 25.1 1.0
CZ A:TYR375 2.9 15.8 1.0
CD2 A:HIS377 3.1 21.7 1.0
CE1 A:HIS377 3.1 23.5 1.0
CE2 A:TYR375 3.2 15.0 1.0
CG A:HIS399 3.3 23.7 1.0
N A:HIS399 3.7 20.2 1.0
CB A:HIS399 3.7 22.1 1.0
NE2 A:HIS399 4.1 24.6 1.0
CE1 A:TYR375 4.1 16.7 1.0
ND1 A:HIS377 4.2 22.9 1.0
CG A:HIS377 4.2 20.3 1.0
CD2 A:HIS399 4.3 25.0 1.0
CA A:HIS399 4.3 22.0 1.0
O A:HOH636 4.5 34.7 1.0
CD2 A:TYR375 4.6 14.7 1.0
C A:LEU398 4.8 20.6 1.0
CA A:LEU398 4.9 20.9 1.0
N A:ALA400 4.9 20.5 1.0
CB A:LEU398 4.9 22.0 1.0

Zinc binding site 2 out of 3 in 5dq0

Go back to Zinc Binding Sites List in 5dq0
Zinc binding site 2 out of 3 in the Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:28.7
occ:1.00
OE2 A:GLU284 1.9 30.2 1.0
CL A:CL504 2.0 37.5 1.0
ND1 A:HIS312 2.2 24.4 1.0
CD A:GLU284 2.7 30.5 1.0
OE1 A:GLU284 2.8 25.2 1.0
CE1 A:HIS312 3.1 25.0 1.0
CG A:HIS312 3.2 22.9 1.0
CB A:HIS312 3.5 23.5 1.0
O A:HOH633 3.9 34.7 1.0
CG A:GLU284 4.1 27.7 1.0
NE2 A:HIS312 4.2 27.3 1.0
CD2 A:HIS312 4.3 26.0 1.0
CA A:HIS312 5.0 25.7 1.0

Zinc binding site 3 out of 3 in 5dq0

Go back to Zinc Binding Sites List in 5dq0
Zinc binding site 3 out of 3 in the Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Neuropilin-2 B1 Domain with Novel and Unique Zinc Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:21.6
occ:0.50
OE1 A:GLU370 2.2 21.9 0.5
O A:HOH718 2.3 32.9 1.0
OE1 A:GLU370 2.3 25.8 0.5
OE2 A:GLU370 2.7 24.4 0.5
CD A:GLU370 2.8 24.3 0.5
CD A:GLU370 3.3 22.6 0.5
OE2 A:GLU370 3.9 24.6 0.5
CG A:GLU370 4.2 24.8 0.5
CG A:GLU370 4.6 21.7 0.5
CB A:GLU370 4.6 21.3 0.5
CB A:GLU370 4.7 23.4 0.5

Reference:

Y.I.Tsai, P.Frankel, R.R.Rana, C.Fotinou, T.S.Yelland, I.Zachary, S.Djordjevic. To Be Published To Be Published.
Page generated: Wed Dec 16 06:08:41 2020

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