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Zinc in PDB 7ufu: Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A (pdb code 7ufu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A, PDB code: 7ufu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7ufu

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:79.2
occ:1.00
OD1 A:ASP277 2.0 56.0 1.0
NE2 A:HIS597 2.1 54.5 1.0
O2 A:MAN1102 2.2 60.7 1.0
O3 A:MAN1102 2.2 60.7 1.0
NE2 A:HIS275 2.3 53.6 1.0
CE1 A:HIS597 2.6 54.5 1.0
C2 A:MAN1102 2.9 60.7 1.0
CG A:ASP277 3.1 56.0 1.0
C3 A:MAN1102 3.1 60.7 1.0
CE1 A:HIS275 3.2 53.6 1.0
CD2 A:HIS275 3.2 53.6 1.0
CD2 A:HIS597 3.3 54.5 1.0
OD2 A:ASP277 3.5 56.0 1.0
ND1 A:HIS597 3.9 54.5 1.0
OD2 A:ASP598 3.9 55.1 1.0
C4 A:MAN1102 4.0 60.7 1.0
CB A:ALA387 4.1 53.3 1.0
CG A:HIS597 4.2 54.5 1.0
ND1 A:HIS275 4.3 53.6 1.0
CB A:ASP277 4.4 56.0 1.0
CG A:HIS275 4.4 53.6 1.0
C1 A:MAN1102 4.4 60.7 1.0
OH A:TYR445 4.8 51.7 1.0
O4 A:MAN1102 4.8 60.7 1.0
CG A:ASP598 4.9 55.1 1.0
CA A:ASP277 4.9 56.0 1.0
CZ A:PHE596 4.9 53.4 1.0
CE2 A:PHE596 5.0 53.4 1.0

Zinc binding site 2 out of 4 in 7ufu

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1101

b:79.5
occ:1.00
OD1 B:ASP277 2.0 55.9 1.0
NE2 B:HIS597 2.1 54.3 1.0
O2 B:MAN1102 2.2 60.5 1.0
O3 B:MAN1102 2.2 60.5 1.0
NE2 B:HIS275 2.3 53.5 1.0
CE1 B:HIS597 2.6 54.3 1.0
C2 B:MAN1102 2.9 60.5 1.0
CG B:ASP277 3.1 55.9 1.0
C3 B:MAN1102 3.1 60.5 1.0
CE1 B:HIS275 3.2 53.5 1.0
CD2 B:HIS275 3.2 53.5 1.0
CD2 B:HIS597 3.3 54.3 1.0
OD2 B:ASP277 3.5 55.9 1.0
ND1 B:HIS597 3.9 54.3 1.0
OD2 B:ASP598 3.9 55.0 1.0
C4 B:MAN1102 4.0 60.5 1.0
CB B:ALA387 4.1 53.3 1.0
CG B:HIS597 4.2 54.3 1.0
ND1 B:HIS275 4.3 53.5 1.0
CB B:ASP277 4.4 55.9 1.0
CG B:HIS275 4.4 53.5 1.0
C1 B:MAN1102 4.4 60.5 1.0
OH B:TYR445 4.8 51.6 1.0
O4 B:MAN1102 4.8 60.5 1.0
CG B:ASP598 4.9 55.0 1.0
CA B:ASP277 4.9 55.9 1.0
CZ B:PHE596 4.9 53.2 1.0
CE2 B:PHE596 5.0 53.2 1.0

Zinc binding site 3 out of 4 in 7ufu

Go back to Zinc Binding Sites List in 7ufu
Zinc binding site 3 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:79.6
occ:1.00
OD1 C:ASP277 2.0 56.2 1.0
NE2 C:HIS597 2.1 54.5 1.0
O2 C:MAN1102 2.2 60.9 1.0
O3 C:MAN1102 2.2 60.9 1.0
NE2 C:HIS275 2.3 53.7 1.0
CE1 C:HIS597 2.6 54.5 1.0
C2 C:MAN1102 2.9 60.9 1.0
CG C:ASP277 3.1 56.2 1.0
C3 C:MAN1102 3.1 60.9 1.0
CE1 C:HIS275 3.2 53.7 1.0
CD2 C:HIS275 3.2 53.7 1.0
CD2 C:HIS597 3.3 54.5 1.0
OD2 C:ASP277 3.5 56.2 1.0
ND1 C:HIS597 3.9 54.5 1.0
OD2 C:ASP598 3.9 55.3 1.0
C4 C:MAN1102 4.0 60.9 1.0
CB C:ALA387 4.1 53.2 1.0
CG C:HIS597 4.2 54.5 1.0
ND1 C:HIS275 4.3 53.7 1.0
CB C:ASP277 4.4 56.2 1.0
CG C:HIS275 4.4 53.7 1.0
C1 C:MAN1102 4.4 60.9 1.0
OH C:TYR445 4.8 51.6 1.0
O4 C:MAN1102 4.8 60.9 1.0
CG C:ASP598 4.9 55.3 1.0
CA C:ASP277 4.9 56.2 1.0
CZ C:PHE596 4.9 53.5 1.0
CE2 C:PHE596 5.0 53.5 1.0

Zinc binding site 4 out of 4 in 7ufu

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1101

b:79.6
occ:1.00
OD1 D:ASP277 2.0 56.1 1.0
NE2 D:HIS597 2.1 54.5 1.0
O2 D:MAN1102 2.2 60.7 1.0
O3 D:MAN1102 2.2 60.7 1.0
NE2 D:HIS275 2.3 53.8 1.0
CE1 D:HIS597 2.6 54.5 1.0
C2 D:MAN1102 2.9 60.7 1.0
CG D:ASP277 3.1 56.1 1.0
C3 D:MAN1102 3.1 60.7 1.0
CE1 D:HIS275 3.2 53.8 1.0
CD2 D:HIS275 3.2 53.8 1.0
CD2 D:HIS597 3.3 54.5 1.0
OD2 D:ASP277 3.5 56.1 1.0
ND1 D:HIS597 3.9 54.5 1.0
OD2 D:ASP598 3.9 55.1 1.0
C4 D:MAN1102 4.0 60.7 1.0
CB D:ALA387 4.1 53.5 1.0
CG D:HIS597 4.2 54.5 1.0
ND1 D:HIS275 4.3 53.8 1.0
CB D:ASP277 4.4 56.1 1.0
CG D:HIS275 4.4 53.8 1.0
C1 D:MAN1102 4.4 60.7 1.0
OH D:TYR445 4.8 51.6 1.0
O4 D:MAN1102 4.8 60.7 1.0
CG D:ASP598 4.9 55.1 1.0
CA D:ASP277 4.9 56.1 1.0
CZ D:PHE596 4.9 53.3 1.0
CE2 D:PHE596 5.0 53.3 1.0

Reference:

C.R.Santos, R.L.Cordeiro, M.N.Domingues, A.C.Borges, M.A.De Farias, M.Van Heel, M.T.Murakami, R.V.Portugal. Cryo-Em Structure of BL_MAN38A Nucleophile Mutant in Complex with Mannose at 2.7 A Nat.Chem.Biol. 2022.
ISSN: ESSN 1552-4469
Page generated: Sat Apr 8 04:12:30 2023

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