Calcium in PDB 6n1b: Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide

Protein crystallography data

The structure of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide, PDB code: 6n1b was solved by L.Sim, P.Rahfeld, S.G.Withers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.40 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.710, 69.240, 104.810, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 16.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide (pdb code 6n1b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide, PDB code: 6n1b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6n1b

Go back to Calcium Binding Sites List in 6n1b
Calcium binding site 1 out of 4 in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:7.1
occ:1.00
OD1 A:ASP100 2.0 12.0 1.0
O A:HOH602 2.0 14.9 1.0
NE2 A:HIS252 2.1 10.2 1.0
O A:HOH696 2.1 10.7 1.0
O A:HOH615 2.1 32.4 1.0
O A:HOH702 2.2 11.4 1.0
CG A:ASP100 3.0 10.3 1.0
CE1 A:HIS252 3.0 7.7 1.0
CD2 A:HIS252 3.2 9.5 1.0
OD2 A:ASP100 3.3 11.2 1.0
SG A:CYS99 3.4 14.7 0.5
O3 A:GLA506 3.8 20.4 1.0
O A:HOH601 3.8 21.6 1.0
O2 A:GLA506 3.9 20.9 1.0
O A:HOH724 4.0 10.6 1.0
C2 A:GLA506 4.1 14.1 1.0
CB A:CYS99 4.1 9.8 0.5
CD2 A:HIS34 4.2 6.3 1.0
OH A:TYR315 4.2 14.1 1.0
ND1 A:HIS252 4.2 7.8 1.0
CB A:CYS99 4.3 10.2 0.5
CG A:HIS252 4.3 8.0 1.0
CB A:ASP100 4.3 9.6 1.0
CE2 A:TYR315 4.3 11.1 1.0
SG A:CYS99 4.5 10.3 0.5
N A:ASP100 4.5 8.1 1.0
C3 A:GLA506 4.6 22.3 1.0
CA A:ASP100 4.6 9.0 1.0
OE2 A:GLU64 4.7 18.3 1.0
NE2 A:HIS34 4.7 11.8 1.0
CZ A:TYR315 4.8 11.5 1.0
NE1 A:TRP251 4.8 9.4 1.0

Calcium binding site 2 out of 4 in 6n1b

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Calcium binding site 2 out of 4 in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:8.8
occ:1.00
O A:HOH617 2.3 12.5 1.0
O A:HOH676 2.4 10.2 1.0
OD1 A:ASP254 2.4 8.3 1.0
OD1 A:ASP36 2.4 8.7 1.0
OD1 A:ASP102 2.4 8.9 1.0
O A:HOH674 2.4 9.8 1.0
OD2 A:ASP36 2.6 8.1 1.0
O A:HOH805 2.8 10.1 1.0
CG A:ASP36 2.8 8.2 1.0
CG A:ASP102 3.4 8.2 1.0
CG A:ASP254 3.4 8.2 1.0
OD2 A:ASP102 3.7 9.9 1.0
OD2 A:ASP254 3.7 10.0 1.0
OG1 A:THR188 4.1 9.4 1.0
O A:MET103 4.3 8.4 1.0
NH2 A:ARG316 4.4 8.4 1.0
CB A:ASP36 4.4 8.0 1.0
NE2 A:GLN256 4.4 14.6 1.0
O A:VAL255 4.5 9.6 1.0
OG A:SER318 4.5 9.4 1.0
O A:HOH905 4.5 15.1 1.0
CB A:ASP102 4.6 9.2 1.0
NH1 A:ARG316 4.7 8.2 1.0
N A:MET103 4.7 8.1 1.0
CB A:ASP254 4.7 8.4 1.0
O A:ILE189 4.8 9.3 1.0
O A:VAL37 4.9 9.3 1.0
O A:HOH694 5.0 11.2 1.0

Calcium binding site 3 out of 4 in 6n1b

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Calcium binding site 3 out of 4 in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:9.1
occ:1.00
ND2 A:ASN236 2.4 7.4 1.0
O A:HOH843 2.4 12.1 1.0
O A:HOH866 2.5 14.8 1.0
CG A:ASN236 3.5 9.2 1.0
CB A:ASN236 4.0 7.7 1.0
CA A:ASN236 4.3 8.3 1.0
NH2 A:ARG234 4.5 17.5 1.0
OD1 A:ASN236 4.5 14.5 1.0
NE A:ARG234 4.6 14.1 1.0
O A:VAL235 4.6 8.7 1.0
O A:HOH796 4.7 18.2 1.0

Calcium binding site 4 out of 4 in 6n1b

Go back to Calcium Binding Sites List in 6n1b
Calcium binding site 4 out of 4 in the Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An N-Acetylgalactosamine Deacetylase From F. Plautii in Complex with Blood Group B Trisaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:11.3
occ:1.00
O A:HOH717 2.4 8.7 1.0
O A:HOH616 2.4 16.3 1.0
O A:HOH760 4.5 14.4 1.0
O A:LEU239 4.6 9.1 1.0
O3 A:GOL508 4.7 22.8 1.0
O A:HOH691 4.8 12.0 1.0
OE1 A:GLN247 4.9 10.4 1.0
O2 A:GOL508 4.9 16.9 1.0
CA A:GLY240 4.9 9.6 1.0

Reference:

P.Rahfeld, L.Sim, H.Moon, I.Constantinescu, C.Morgan-Lang, S.J.Hallam, J.N.Kizhakkedathu, S.G.Withers. An Enzymatic Pathway in the Human Gut Microbiome That Converts A to Universal O Type Blood. Nat Microbiol V. 4 1475 2019.
ISSN: ESSN 2058-5276
PubMed: 31182795
DOI: 10.1038/S41564-019-0469-7
Page generated: Sat Dec 12 07:18:52 2020

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