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Manganese in PDB 6pxu: Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

Enzymatic activity of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

All present enzymatic activity of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp:
2.4.1.41;

Protein crystallography data

The structure of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp, PDB code: 6pxu was solved by N.L.Samara, A.J.Fernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.03 / 2.01
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.820, 73.123, 74.441, 113.08, 100.50, 108.23
R / Rfree (%) 17.1 / 21.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp (pdb code 6pxu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp, PDB code: 6pxu:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6pxu

Go back to Manganese Binding Sites List in 6pxu
Manganese binding site 1 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn610

b:32.1
occ:1.00
 O2A A:UDP601 2.1 28.4 1.0
NE2 A:HIS363 2.2 29.8 1.0
O3B A:UDP601 2.2 32.8 1.0
NE2 A:HIS230 2.3 31.3 1.0
OD2 A:ASP228 2.3 36.6 1.0
O A:HOH726 2.4 32.2 1.0
CE1 A:HIS363 3.0 34.0 1.0
PB A:UDP601 3.2 34.5 1.0
CE1 A:HIS230 3.2 34.0 1.0
CD2 A:HIS230 3.2 22.9 1.0
CG A:ASP228 3.3 32.7 1.0
CD2 A:HIS363 3.3 27.5 1.0
PA A:UDP601 3.3 29.3 1.0
O2B A:UDP601 3.5 32.5 1.0
O3A A:UDP601 3.7 31.9 1.0
O5' A:UDP601 3.7 41.1 1.0
CB A:ASP228 3.8 29.5 1.0
ND1 A:HIS363 4.1 35.8 1.0
CG A:HIS363 4.3 30.2 1.0
ND1 A:HIS230 4.3 31.7 1.0
OD1 A:ASP228 4.3 39.0 1.0
CG A:HIS230 4.4 29.3 1.0
O1A A:UDP601 4.5 28.1 1.0
O1B A:UDP601 4.5 31.0 1.0
O A:HOH826 4.6 44.8 1.0
C3' A:UDP601 4.9 28.3 1.0

Manganese binding site 2 out of 4 in 6pxu

Go back to Manganese Binding Sites List in 6pxu
Manganese binding site 2 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn611

b:31.1
occ:0.80
 O A:HOH775 2.3 25.9 1.0
O A:VAL197 2.4 22.4 1.0
O A:HOH750 2.5 21.4 1.0
C A:VAL197 3.6 24.1 1.0
O A:HOH920 4.0 33.9 1.0
O A:LEU194 4.2 21.1 1.0
N A:VAL197 4.3 23.3 1.0
CA A:VAL197 4.5 22.3 1.0
N A:ARG198 4.5 18.1 1.0
CA A:ARG198 4.6 21.1 1.0
O A:SER192 4.7 27.1 1.0
CG A:ARG198 4.8 20.6 1.0
CB A:VAL197 4.9 23.1 1.0
O A:HOH923 4.9 20.6 1.0

Manganese binding site 3 out of 4 in 6pxu

Go back to Manganese Binding Sites List in 6pxu
Manganese binding site 3 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:30.6
occ:1.00
 O1A B:UDP602 2.2 28.1 1.0
OD2 B:ASP228 2.3 41.1 1.0
O1B B:UDP602 2.3 31.4 1.0
NE2 B:HIS363 2.3 28.5 1.0
NE2 B:HIS230 2.3 34.5 1.0
O B:HOH815 2.4 41.0 1.0
CE1 B:HIS363 3.1 34.5 1.0
PB B:UDP602 3.2 31.4 1.0
CE1 B:HIS230 3.3 35.6 1.0
CG B:ASP228 3.3 35.4 1.0
CD2 B:HIS230 3.3 30.7 1.0
CD2 B:HIS363 3.4 31.8 1.0
PA B:UDP602 3.4 29.3 1.0
O2B B:UDP602 3.5 33.0 1.0
O3A B:UDP602 3.7 30.5 1.0
CB B:ASP228 3.8 26.9 1.0
C5' B:UDP602 4.2 26.0 1.0
O5' B:UDP602 4.3 25.6 1.0
OD1 B:ASP228 4.3 33.5 1.0
ND1 B:HIS363 4.3 35.4 1.0
O B:HOH890 4.3 37.3 1.0
ND1 B:HIS230 4.4 31.0 1.0
CG B:HIS230 4.4 32.4 1.0
CG B:HIS363 4.5 29.3 1.0
O2A B:UDP602 4.5 32.0 1.0
O3B B:UDP602 4.6 29.2 1.0
C3' B:UDP602 4.6 32.2 1.0
C4' B:UDP602 5.0 29.4 1.0

Manganese binding site 4 out of 4 in 6pxu

Go back to Manganese Binding Sites List in 6pxu
Manganese binding site 4 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn615

b:82.2
occ:0.50
 OH B:TYR145 2.2 44.7 1.0
OD2 B:ASP179 2.2 65.6 1.0
O B:HOH823 2.6 46.2 1.0
CZ B:TYR145 3.1 37.3 1.0
CE1 B:TYR145 3.3 32.8 1.0
CG B:ASP179 3.4 57.7 1.0
O B:HOH846 3.5 51.1 1.0
ND2 B:ASN146 3.6 38.9 1.0
CB B:ASP179 4.2 44.4 1.0
CE2 B:TYR145 4.3 35.2 1.0
OD1 B:ASP179 4.3 69.9 1.0
CG B:ASN146 4.5 33.1 1.0
N B:ASP179 4.6 30.0 1.0
O B:TYR177 4.6 30.5 1.0
CD1 B:TYR145 4.6 24.0 1.0
OD1 B:ASN146 4.6 29.7 1.0
NH1 B:ARG205 4.7 49.5 1.0

Reference:

A.J.Fernandez, E.J.P.Daniel, S.P.Mahajan, J.J.Gray, T.A.Gerken, L.A.Tabak, N.L.Samara. The Structure of the Colorectal Cancer-Associated Enzyme Galnac-T12 Reveals How Nonconserved Residues Dictate Its Function. Proc.Natl.Acad.Sci.Usa V. 116 20404 2019.
ISSN: ESSN 1091-6490
PubMed: 31548401
DOI: 10.1073/PNAS.1902211116
Page generated: Sun Oct 6 05:52:42 2024

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