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Manganese in PDB 4d0t: Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese

Enzymatic activity of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese

All present enzymatic activity of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese:
2.4.1.41;

Protein crystallography data

The structure of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese, PDB code: 4d0t was solved by E.Lira-Navarrete, J.Iglesias-Fernandez, W.F.Zandberg, I.Companon, Y.Kong, F.Corzana, B.M.Pinto, H.Clausen, J.M.Peregrina, D.Vocadlo, C.Rovira, R.Hurtado-Guerrero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 249.72 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.217, 122.372, 249.724, 90.00, 90.00, 90.00
R / Rfree (%) 21.351 / 24.116

Manganese Binding Sites:

The binding sites of Manganese atom in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese (pdb code 4d0t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese, PDB code: 4d0t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4d0t

Go back to Manganese Binding Sites List in 4d0t
Manganese binding site 1 out of 6 in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1571

b:25.7
occ:1.00
 O2A A:UD21574 2.1 25.9 1.0
O2B A:UD21574 2.2 27.0 1.0
OD2 A:ASP224 2.2 25.6 1.0
NE2 A:HIS226 2.2 24.1 1.0
NE2 A:HIS359 2.2 26.3 1.0
O A:HOH2049 2.3 23.8 1.0
CE1 A:HIS226 3.1 24.3 1.0
CE1 A:HIS359 3.1 25.9 1.0
CD2 A:HIS226 3.2 24.3 1.0
CG A:ASP224 3.3 25.7 1.0
PB A:UD21574 3.3 27.7 1.0
PA A:UD21574 3.3 27.3 1.0
CD2 A:HIS359 3.3 26.2 1.0
O3A A:UD21574 3.6 27.4 1.0
CB A:ASP224 3.8 25.4 1.0
O5B A:UD21574 3.9 29.5 1.0
O1' A:UD21574 4.1 40.6 1.0
N2' A:UD21574 4.2 36.0 1.0
ND1 A:HIS226 4.3 24.4 1.0
ND1 A:HIS359 4.3 26.4 1.0
OD1 A:ASP224 4.4 25.9 1.0
CG A:HIS226 4.4 24.6 1.0
O A:VAL360 4.4 28.9 1.0
CG A:HIS359 4.4 26.4 1.0
O1A A:UD21574 4.6 30.0 1.0
C8' A:UD21574 4.6 30.2 1.0
O1B A:UD21574 4.7 34.5 1.0
C3B A:UD21574 4.8 25.7 1.0
C5B A:UD21574 4.9 28.5 1.0
C4B A:UD21574 4.9 25.0 1.0
NH2 A:ARG362 5.0 36.4 1.0

Manganese binding site 2 out of 6 in 4d0t

Go back to Manganese Binding Sites List in 4d0t
Manganese binding site 2 out of 6 in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1570

b:34.8
occ:1.00
 O2B B:UD21573 1.9 37.0 1.0
O2A B:UD21573 2.1 36.4 1.0
OD2 B:ASP224 2.1 29.5 1.0
NE2 B:HIS359 2.3 32.4 1.0
NE2 B:HIS226 2.3 30.7 1.0
CE1 B:HIS359 3.1 32.9 1.0
PB B:UD21573 3.2 36.6 1.0
CE1 B:HIS226 3.2 30.9 1.0
PA B:UD21573 3.3 36.6 1.0
CG B:ASP224 3.3 29.9 1.0
CD2 B:HIS226 3.4 30.4 1.0
CD2 B:HIS359 3.4 32.3 1.0
O3A B:UD21573 3.5 41.3 1.0
O5B B:UD21573 3.7 34.0 1.0
CB B:ASP224 3.8 29.1 1.0
O1B B:UD21573 4.2 45.0 1.0
N2' B:UD21573 4.2 47.5 1.0
O1' B:UD21573 4.2 47.8 1.0
ND1 B:HIS359 4.3 33.3 1.0
OD1 B:ASP224 4.4 30.4 1.0
ND1 B:HIS226 4.4 31.2 1.0
O B:VAL360 4.5 37.5 1.0
CG B:HIS226 4.5 31.1 1.0
CG B:HIS359 4.5 32.0 1.0
O1A B:UD21573 4.6 37.6 1.0
C8' B:UD21573 4.6 35.7 1.0
C5B B:UD21573 4.8 36.9 1.0
C3B B:UD21573 4.9 40.8 1.0
NH2 B:ARG362 5.0 48.6 1.0

Manganese binding site 3 out of 6 in 4d0t

Go back to Manganese Binding Sites List in 4d0t
Manganese binding site 3 out of 6 in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1570

b:29.9
occ:1.00
 OD2 C:ASP224 2.1 27.3 1.0
O2B C:UDP1571 2.2 34.7 1.0
O1A C:UDP1571 2.2 31.3 1.0
NE2 C:HIS226 2.2 26.6 1.0
O C:HOH2027 2.3 34.2 1.0
NE2 C:HIS359 2.3 28.1 1.0
CE1 C:HIS226 3.1 27.1 1.0
CE1 C:HIS359 3.1 28.9 1.0
PB C:UDP1571 3.2 34.3 1.0
CG C:ASP224 3.3 26.7 1.0
CD2 C:HIS226 3.3 27.6 1.0
CD2 C:HIS359 3.4 28.6 1.0
PA C:UDP1571 3.4 32.9 1.0
O1B C:UDP1571 3.5 38.0 1.0
O3A C:UDP1571 3.6 32.9 1.0
CB C:ASP224 3.8 26.8 1.0
C5' C:UDP1571 4.2 33.4 1.0
ND1 C:HIS226 4.3 27.5 1.0
O5' C:UDP1571 4.3 33.7 1.0
ND1 C:HIS359 4.3 29.2 1.0
OD1 C:ASP224 4.3 25.9 1.0
CG C:HIS226 4.4 27.7 1.0
O C:VAL360 4.4 34.9 1.0
CG C:HIS359 4.5 28.4 1.0
N2 P:NGA1572 4.5 44.0 1.0
O3B C:UDP1571 4.6 35.5 1.0
O2A C:UDP1571 4.7 32.1 1.0
O C:HOH2046 4.7 36.9 1.0
O3 P:NGA1572 4.8 46.1 1.0
C3' C:UDP1571 4.9 33.5 1.0
C8 P:NGA1572 4.9 42.0 1.0
C4' C:UDP1571 4.9 33.2 1.0
C3 P:NGA1572 5.0 45.9 1.0
NH2 C:ARG362 5.0 40.9 1.0

Manganese binding site 4 out of 6 in 4d0t

Go back to Manganese Binding Sites List in 4d0t
Manganese binding site 4 out of 6 in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1570

b:32.3
occ:1.00
 O2B D:UD21571 2.0 39.2 1.0
O2A D:UD21571 2.0 40.6 1.0
NE2 D:HIS359 2.2 36.4 1.0
NE2 D:HIS226 2.2 33.1 1.0
OD2 D:ASP224 2.2 34.3 1.0
CE1 D:HIS359 3.0 36.0 1.0
CE1 D:HIS226 3.1 33.9 1.0
PB D:UD21571 3.2 37.0 1.0
CD2 D:HIS226 3.2 33.0 1.0
PA D:UD21571 3.3 35.4 1.0
CD2 D:HIS359 3.3 36.2 1.0
CG D:ASP224 3.4 32.6 1.0
O3A D:UD21571 3.6 30.2 1.0
CB D:ASP224 3.8 31.4 1.0
O5B D:UD21571 3.9 42.0 1.0
O1' D:UD21571 4.1 47.4 1.0
ND1 D:HIS359 4.2 36.4 1.0
N2' D:UD21571 4.2 35.4 1.0
ND1 D:HIS226 4.3 33.7 1.0
O D:HOH2041 4.3 36.4 1.0
O D:VAL360 4.3 37.8 1.0
CG D:HIS359 4.3 35.5 1.0
CG D:HIS226 4.4 32.9 1.0
OD1 D:ASP224 4.4 33.4 1.0
O1B D:UD21571 4.5 41.3 1.0
O1A D:UD21571 4.6 36.0 1.0
C8' D:UD21571 4.8 38.4 1.0
C5B D:UD21571 4.8 36.2 1.0
C4B D:UD21571 5.0 34.5 1.0
C1' D:UD21571 5.0 40.1 1.0
C3B D:UD21571 5.0 35.9 1.0
C7' D:UD21571 5.0 37.1 1.0

Manganese binding site 5 out of 6 in 4d0t

Go back to Manganese Binding Sites List in 4d0t
Manganese binding site 5 out of 6 in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1570

b:29.6
occ:1.00
 O2A E:UD21571 1.8 33.2 1.0
O2B E:UD21571 2.0 30.1 1.0
OD2 E:ASP224 2.2 22.6 1.0
NE2 E:HIS226 2.2 22.5 1.0
NE2 E:HIS359 2.3 24.5 1.0
O E:HOH2053 2.4 24.8 1.0
CE1 E:HIS226 3.1 23.0 1.0
CE1 E:HIS359 3.1 24.9 1.0
PA E:UD21571 3.1 30.6 1.0
CG E:ASP224 3.3 22.3 1.0
CD2 E:HIS226 3.3 22.6 1.0
PB E:UD21571 3.3 28.6 1.0
CD2 E:HIS359 3.4 24.4 1.0
O3A E:UD21571 3.6 32.2 1.0
O5B E:UD21571 3.7 35.6 1.0
CB E:ASP224 3.8 22.4 1.0
N2' E:UD21571 4.1 42.6 1.0
ND1 E:HIS226 4.3 23.1 1.0
ND1 E:HIS359 4.3 24.9 1.0
OD1 E:ASP224 4.4 22.5 1.0
O1A E:UD21571 4.4 33.1 1.0
CG E:HIS226 4.4 23.0 1.0
O1' E:UD21571 4.4 39.3 1.0
O E:VAL360 4.4 26.3 1.0
CG E:HIS359 4.5 24.4 1.0
C8' E:UD21571 4.5 34.0 1.0
O1B E:UD21571 4.6 38.8 1.0
C3B E:UD21571 4.8 27.4 1.0
C5B E:UD21571 4.8 33.8 1.0
C4B E:UD21571 4.9 29.2 1.0
C7' E:UD21571 4.9 32.8 1.0
NH2 E:ARG362 4.9 30.9 1.0

Manganese binding site 6 out of 6 in 4d0t

Go back to Manganese Binding Sites List in 4d0t
Manganese binding site 6 out of 6 in the Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Galnac-T2 Crystal Soaked with Udp-Galnac, EA2 Peptide and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1566

b:40.9
occ:1.00
 O2A F:UD21567 2.0 51.8 1.0
O2B F:UD21567 2.1 48.0 1.0
OD2 F:ASP224 2.1 37.9 1.0
NE2 F:HIS359 2.2 36.3 1.0
NE2 F:HIS226 2.3 34.1 1.0
CE1 F:HIS359 3.0 36.8 1.0
CE1 F:HIS226 3.2 35.7 1.0
CG F:ASP224 3.3 36.9 1.0
CD2 F:HIS359 3.3 35.9 1.0
PA F:UD21567 3.3 47.0 1.0
CD2 F:HIS226 3.3 33.6 1.0
PB F:UD21567 3.4 48.5 1.0
CB F:ASP224 3.8 35.0 1.0
O5B F:UD21567 3.8 44.6 1.0
O3A F:UD21567 3.8 45.7 1.0
N2' F:UD21567 4.0 60.7 1.0
ND1 F:HIS359 4.2 36.3 1.0
OD1 F:ASP224 4.3 37.9 1.0
CG F:HIS359 4.3 35.7 1.0
ND1 F:HIS226 4.4 35.3 1.0
O F:VAL360 4.4 36.5 1.0
C8' F:UD21567 4.4 47.0 1.0
CG F:HIS226 4.5 34.1 1.0
O1' F:UD21567 4.5 58.8 1.0
O1A F:UD21567 4.5 47.6 1.0
O1B F:UD21567 4.5 54.2 1.0
C7' F:UD21567 4.8 50.5 1.0
C5B F:UD21567 4.8 44.9 1.0
C3' F:UD21567 4.9 64.8 1.0
C3B F:UD21567 4.9 40.0 1.0
C2' F:UD21567 4.9 66.2 1.0
O3' F:UD21567 5.0 58.2 1.0
C4B F:UD21567 5.0 42.2 1.0

Reference:

E.Lira-Navarrete, J.Iglesias-Fernandez, W.F.Zandberg, I.Companon, Y.Kong, F.Corzana, B.M.Pinto, H.Clausen, J.M.Peregrina, D.Vocadlo, C.Rovira, R.Hurtado-Guerrero. Substrate-Guided Front-Face Reaction Revealed By Combined Structural Snapshots and Metadynamics For the Polypeptide N- Acetylgalactosaminyltransferase 2. Angew.Chem.Int.Ed.Engl. V. 53 8206 2014.
ISSN: ISSN 1433-7851
PubMed: 24954443
DOI: 10.1002/ANIE.201402781
Page generated: Tue Dec 15 04:19:03 2020

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