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Manganese in PDB 4d11: Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset)

Protein crystallography data

The structure of Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset), PDB code: 4d11 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) 249.61 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.771, 120.898, 249.607, 90.00, 90.00, 90.00
R / Rfree (%) 21.602 / 23.497

Manganese Binding Sites:

The binding sites of Manganese atom in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset) (pdb code 4d11). 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-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset), PDB code: 4d11:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4d11

Go back to Manganese Binding Sites List in 4d11
Manganese binding site 1 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset)


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-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1570

b:46.8
occ:1.00
 O2A A:UDP1572 1.8 66.4 1.0
OD2 A:ASP224 1.8 33.9 1.0
O3B A:UDP1572 2.1 58.6 1.0
NE2 A:HIS226 2.2 30.6 1.0
NE2 A:HIS359 2.4 28.4 1.0
CE1 A:HIS226 3.1 30.8 1.0
PB A:UDP1572 3.1 58.6 1.0
PA A:UDP1572 3.1 60.8 1.0
CG A:ASP224 3.1 33.6 1.0
CE1 A:HIS359 3.2 28.4 1.0
CD2 A:HIS226 3.3 30.3 1.0
CD2 A:HIS359 3.5 28.4 1.0
O3A A:UDP1572 3.5 55.8 1.0
O5' A:UDP1572 3.6 71.3 1.0
O2B A:UDP1572 3.8 79.6 1.0
OD1 A:ASP224 3.9 35.7 1.0
CB A:ASP224 4.1 32.4 1.0
ND1 A:HIS226 4.2 30.6 1.0
O1A A:UDP1572 4.3 54.0 1.0
CG A:HIS226 4.4 30.3 1.0
O1B A:UDP1572 4.4 68.8 1.0
O A:VAL360 4.4 31.8 1.0
ND1 A:HIS359 4.4 28.5 1.0
C3' A:UDP1572 4.5 87.3 1.0
CG A:HIS359 4.6 28.4 1.0
NH2 A:ARG362 4.8 54.1 1.0
C5' A:UDP1572 4.8 76.0 1.0
C4' A:UDP1572 4.9 87.2 1.0
O3' A:UDP1572 4.9 87.3 1.0

Manganese binding site 2 out of 6 in 4d11

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Manganese binding site 2 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset)


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-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1571

b:64.0
occ:1.00
 OD2 B:ASP224 1.8 71.8 1.0
O3B B:UDP1573 2.0 89.5 1.0
NE2 B:HIS226 2.1 55.1 1.0
NE2 B:HIS359 2.4 58.9 1.0
CE1 B:HIS226 3.0 56.4 1.0
O2A B:UDP1573 3.0 77.8 1.0
CG B:ASP224 3.1 67.6 1.0
O5' B:UDP1573 3.1 80.7 1.0
CD2 B:HIS226 3.1 54.2 1.0
CE1 B:HIS359 3.2 57.5 1.0
PB B:UDP1573 3.2 90.6 1.0
CD2 B:HIS359 3.4 56.9 1.0
PA B:UDP1573 3.5 79.9 1.0
O3A B:UDP1573 3.7 91.1 1.0
OD1 B:ASP224 4.0 72.6 1.0
O2B B:UDP1573 4.0 93.9 1.0
CB B:ASP224 4.0 59.8 1.0
ND1 B:HIS226 4.1 56.7 1.0
CG B:HIS226 4.2 55.0 1.0
C5' B:UDP1573 4.4 84.3 1.0
ND1 B:HIS359 4.4 55.4 1.0
O B:VAL360 4.4 55.6 1.0
O1B B:UDP1573 4.5 87.2 1.0
CG B:HIS359 4.5 52.9 1.0
C3' B:UDP1573 4.7 92.2 1.0
NH2 B:ARG362 4.8 93.6 1.0
O1A B:UDP1573 4.9 97.7 1.0

Manganese binding site 3 out of 6 in 4d11

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Manganese binding site 3 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset)


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-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1570

b:67.4
occ:1.00
 OD2 C:ASP224 1.7 64.7 1.0
O3B C:UDP1571 1.9 0.2 1.0
O2A C:UDP1571 2.1 88.1 1.0
NE2 C:HIS226 2.2 55.5 1.0
NE2 C:HIS359 2.2 61.7 1.0
CG C:ASP224 3.0 61.4 1.0
CE1 C:HIS359 3.1 64.1 1.0
CE1 C:HIS226 3.1 54.6 1.0
CD2 C:HIS226 3.2 54.9 1.0
PA C:UDP1571 3.2 95.5 1.0
PB C:UDP1571 3.3 0.6 1.0
CD2 C:HIS359 3.3 60.4 1.0
O3A C:UDP1571 3.6 94.9 1.0
O5' C:UDP1571 3.6 95.6 1.0
OD1 C:ASP224 3.9 65.2 1.0
CB C:ASP224 4.0 55.8 1.0
O2B C:UDP1571 4.2 0.0 1.0
ND1 C:HIS359 4.3 64.5 1.0
ND1 C:HIS226 4.3 52.6 1.0
CG C:HIS226 4.3 52.0 1.0
O C:VAL360 4.4 66.8 1.0
CG C:HIS359 4.4 60.6 1.0
O1B C:UDP1571 4.4 0.8 1.0
O1A C:UDP1571 4.6 93.7 1.0
C3' C:UDP1571 4.7 0.8 1.0
C5' C:UDP1571 4.9 95.2 1.0

Manganese binding site 4 out of 6 in 4d11

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Manganese binding site 4 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset)


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-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1570

b:58.7
occ:1.00
 OD2 D:ASP224 1.9 44.7 1.0
O2A D:UDP1571 2.0 81.9 1.0
O3B D:UDP1571 2.0 0.5 1.0
NE2 D:HIS359 2.2 32.3 1.0
NE2 D:HIS226 2.3 35.0 1.0
CE1 D:HIS359 3.0 32.4 1.0
CG D:ASP224 3.2 43.2 1.0
PB D:UDP1571 3.2 98.7 1.0
PA D:UDP1571 3.2 78.6 1.0
CD2 D:HIS226 3.3 34.7 1.0
CE1 D:HIS226 3.3 35.1 1.0
CD2 D:HIS359 3.3 31.9 1.0
O5' D:UDP1571 3.5 80.5 1.0
O3A D:UDP1571 3.7 95.3 1.0
O2B D:UDP1571 3.8 86.1 1.0
OD1 D:ASP224 4.0 47.8 1.0
CB D:ASP224 4.1 39.7 1.0
ND1 D:HIS359 4.2 31.9 1.0
CG D:HIS359 4.4 31.2 1.0
O D:VAL360 4.4 38.9 1.0
ND1 D:HIS226 4.4 34.9 1.0
CG D:HIS226 4.4 34.4 1.0
O1B D:UDP1571 4.5 92.7 1.0
O1A D:UDP1571 4.5 76.9 1.0
C5' D:UDP1571 4.9 92.0 1.0
C3' D:UDP1571 4.9 0.3 1.0

Manganese binding site 5 out of 6 in 4d11

Go back to Manganese Binding Sites List in 4d11
Manganese binding site 5 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset)


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-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1570

b:46.4
occ:1.00
 O3B E:UDP1572 1.6 93.2 1.0
OD2 E:ASP224 1.8 42.8 1.0
O2A E:UDP1572 2.0 76.2 1.0
NE2 E:HIS226 2.1 34.3 1.0
NE2 E:HIS359 2.3 34.0 1.0
PB E:UDP1572 3.0 87.8 1.0
CE1 E:HIS226 3.0 34.0 1.0
CG E:ASP224 3.1 42.8 1.0
CD2 E:HIS226 3.1 34.1 1.0
CE1 E:HIS359 3.1 34.2 1.0
PA E:UDP1572 3.3 76.0 1.0
CD2 E:HIS359 3.3 33.9 1.0
O3A E:UDP1572 3.6 88.6 1.0
O5' E:UDP1572 3.7 70.8 1.0
O2B E:UDP1572 3.9 89.7 1.0
OD1 E:ASP224 3.9 46.7 1.0
CB E:ASP224 4.0 39.5 1.0
O1B E:UDP1572 4.1 97.5 1.0
ND1 E:HIS226 4.2 33.8 1.0
CG E:HIS226 4.2 34.3 1.0
ND1 E:HIS359 4.3 34.6 1.0
O E:VAL360 4.3 45.5 1.0
CG E:HIS359 4.4 34.2 1.0
O1A E:UDP1572 4.6 83.7 1.0
C3' E:UDP1572 4.8 80.6 1.0
NH2 E:ARG362 4.8 64.3 1.0

Manganese binding site 6 out of 6 in 4d11

Go back to Manganese Binding Sites List in 4d11
Manganese binding site 6 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset)


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-5SGALNAC, MEA2 Peptide and Manganese (Lower Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1363

b:93.5
occ:1.00
 O2A F:UDP1364 1.8 0.2 1.0
OD2 F:ASP224 1.8 0.6 1.0
NE2 F:HIS359 2.2 96.6 1.0
NE2 F:HIS226 2.2 72.8 1.0
O3B F:UDP1364 2.6 0.3 1.0
CE1 F:HIS359 3.0 0.7 1.0
CG F:ASP224 3.1 93.2 1.0
CE1 F:HIS226 3.1 75.3 1.0
PA F:UDP1364 3.1 0.2 1.0
CD2 F:HIS226 3.2 75.2 1.0
CD2 F:HIS359 3.3 93.7 1.0
PB F:UDP1364 3.3 0.2 1.0
O2B F:UDP1364 3.5 0.9 1.0
O5' F:UDP1364 3.6 0.4 1.0
O3A F:UDP1364 3.7 0.2 1.0
OD1 F:ASP224 3.9 93.7 1.0
CB F:ASP224 4.1 86.3 1.0
ND1 F:HIS359 4.2 98.0 1.0
ND1 F:HIS226 4.3 76.8 1.0
CG F:HIS226 4.3 78.5 1.0
O F:VAL360 4.3 87.5 1.0
CG F:HIS359 4.3 92.1 1.0
O1A F:UDP1364 4.4 0.0 1.0
NH2 F:ARG362 4.6 0.9 1.0
C3' F:UDP1364 4.6 0.5 1.0
O1B F:UDP1364 4.8 0.2 1.0
O3' F:UDP1364 4.8 0.3 1.0
C5' F:UDP1364 4.8 0.2 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: Sat Oct 5 18:57:45 2024

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