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Manganese in PDB 4d0z: Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher Resolution Dataset)

Enzymatic activity of Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher Resolution Dataset)

All present enzymatic activity of Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher Resolution Dataset):
2.4.1.41;

Protein crystallography data

The structure of Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher Resolution Dataset), PDB code: 4d0z 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) 249.39 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.485, 121.143, 249.387, 90.00, 90.00, 90.00
R / Rfree (%) 19.641 / 23.377

Manganese Binding Sites:

The binding sites of Manganese atom in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher Resolution Dataset) (pdb code 4d0z). 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 and Manganese (Higher Resolution Dataset), PDB code: 4d0z:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4d0z

Go back to Manganese Binding Sites List in 4d0z
Manganese binding site 1 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher 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 and Manganese (Higher Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1570

b:27.1
occ:1.00
 O2B A:HWU1582 1.9 34.8 1.0
O2A A:HWU1582 2.1 26.5 1.0
NE2 A:HIS226 2.2 24.0 1.0
OD2 A:ASP224 2.2 27.9 1.0
O A:HOH2067 2.3 28.2 1.0
NE2 A:HIS359 2.4 30.1 1.0
CE1 A:HIS226 3.1 24.7 1.0
PB A:HWU1582 3.2 36.0 1.0
CE1 A:HIS359 3.3 28.8 1.0
CD2 A:HIS226 3.3 25.3 1.0
CG A:ASP224 3.3 30.9 1.0
PA A:HWU1582 3.3 32.0 1.0
CD2 A:HIS359 3.4 28.9 1.0
O3A A:HWU1582 3.6 28.7 1.0
CB A:ASP224 3.8 30.7 1.0
N2' A:HWU1582 4.2 43.5 1.0
ND1 A:HIS226 4.2 24.8 1.0
O1B A:HWU1582 4.3 41.0 1.0
O1' A:HWU1582 4.3 43.6 1.0
C5B A:HWU1582 4.3 33.8 1.0
O A:VAL360 4.4 29.9 1.0
CG A:HIS226 4.4 25.6 1.0
OD1 A:ASP224 4.4 31.9 1.0
ND1 A:HIS359 4.4 29.2 1.0
O5B A:HWU1582 4.4 31.2 1.0
O1A A:HWU1582 4.5 27.9 1.0
CG A:HIS359 4.5 27.8 1.0
C8' A:HWU1582 4.6 45.0 1.0
O A:HOH2096 4.6 29.8 1.0
C3B A:HWU1582 4.8 33.2 1.0
NH2 A:ARG362 4.9 37.0 1.0
C7' A:HWU1582 5.0 43.0 1.0

Manganese binding site 2 out of 6 in 4d0z

Go back to Manganese Binding Sites List in 4d0z
Manganese binding site 2 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher 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 and Manganese (Higher Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1570

b:33.7
occ:1.00
 O2A B:HWU1571 2.0 30.8 1.0
O2B B:HWU1571 2.2 31.5 1.0
OD2 B:ASP224 2.2 40.0 1.0
NE2 B:HIS226 2.2 29.5 1.0
O B:HOH2044 2.3 32.9 1.0
NE2 B:HIS359 2.4 34.4 1.0
CE1 B:HIS226 3.1 30.6 1.0
CE1 B:HIS359 3.2 30.6 1.0
CG B:ASP224 3.3 38.4 1.0
CD2 B:HIS226 3.3 30.2 1.0
PA B:HWU1571 3.3 33.3 1.0
PB B:HWU1571 3.4 36.7 1.0
CD2 B:HIS359 3.4 31.5 1.0
O5B B:HWU1571 3.5 39.9 1.0
O3A B:HWU1571 3.7 37.1 1.0
CB B:ASP224 3.8 37.0 1.0
O1B B:HWU1571 4.1 49.7 1.0
ND1 B:HIS226 4.3 31.1 1.0
N2' B:HWU1571 4.3 43.2 1.0
OD1 B:ASP224 4.4 40.2 1.0
O B:VAL360 4.4 33.5 1.0
ND1 B:HIS359 4.4 30.2 1.0
CG B:HIS226 4.4 30.7 1.0
C8' B:HWU1571 4.5 44.7 1.0
CG B:HIS359 4.5 31.5 1.0
O1' B:HWU1571 4.5 47.9 1.0
O1A B:HWU1571 4.6 30.2 1.0
O B:HOH2078 4.7 35.7 1.0
C5B B:HWU1571 4.8 31.8 1.0
C3B B:HWU1571 4.9 34.3 1.0
NH2 B:ARG362 4.9 44.6 1.0

Manganese binding site 3 out of 6 in 4d0z

Go back to Manganese Binding Sites List in 4d0z
Manganese binding site 3 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher 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 and Manganese (Higher Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1570

b:59.4
occ:1.00
 NE2 C:HIS226 1.9 72.2 1.0
O2B C:HWU1569 2.1 53.1 1.0
NE2 C:HIS359 2.3 70.6 1.0
O2A C:HWU1569 2.5 54.6 1.0
OD2 C:ASP224 2.6 73.4 1.0
CE1 C:HIS226 2.9 68.7 1.0
PB C:HWU1569 2.9 56.3 1.0
CD2 C:HIS226 3.0 71.7 1.0
O1B C:HWU1569 3.0 51.6 1.0
CD2 C:HIS359 3.3 66.1 1.0
CE1 C:HIS359 3.3 69.2 1.0
PA C:HWU1569 3.5 77.9 1.0
CG C:ASP224 3.7 66.8 1.0
O3A C:HWU1569 3.7 62.1 1.0
ND1 C:HIS226 4.0 72.3 1.0
CG C:HIS226 4.1 72.8 1.0
CB C:ASP224 4.1 67.5 1.0
O C:VAL360 4.1 72.2 1.0
O1' C:HWU1569 4.2 78.6 1.0
ND1 C:HIS359 4.4 65.5 1.0
CG C:HIS359 4.4 65.9 1.0
O5B C:HWU1569 4.5 66.0 1.0
O1A C:HWU1569 4.5 92.4 1.0
C5B C:HWU1569 4.5 70.7 1.0
C8' C:HWU1569 4.6 89.5 1.0
OD1 C:ASP224 4.7 65.3 1.0
C3B C:HWU1569 4.8 73.6 1.0
NH2 C:ARG362 4.8 85.4 1.0
N2' C:HWU1569 4.8 84.0 1.0

Manganese binding site 4 out of 6 in 4d0z

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Manganese binding site 4 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher 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 and Manganese (Higher Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1570

b:29.1
occ:1.00
 O2B D:HWU1571 2.0 37.5 1.0
O2A D:HWU1571 2.1 34.0 1.0
OD2 D:ASP224 2.2 28.8 1.0
NE2 D:HIS359 2.3 26.1 1.0
NE2 D:HIS226 2.3 27.7 1.0
O D:HOH2052 2.3 32.2 1.0
CE1 D:HIS359 3.2 26.8 1.0
CE1 D:HIS226 3.2 29.1 1.0
PB D:HWU1571 3.3 36.4 1.0
CD2 D:HIS359 3.3 27.8 1.0
CG D:ASP224 3.3 27.8 1.0
CD2 D:HIS226 3.4 28.3 1.0
PA D:HWU1571 3.4 31.2 1.0
O3A D:HWU1571 3.5 24.4 1.0
CB D:ASP224 3.8 28.4 1.0
O5B D:HWU1571 4.1 37.3 1.0
N2' D:HWU1571 4.1 46.0 1.0
O1' D:HWU1571 4.3 37.2 1.0
ND1 D:HIS359 4.3 28.7 1.0
ND1 D:HIS226 4.4 28.8 1.0
OD1 D:ASP224 4.4 26.6 1.0
O D:VAL360 4.4 32.8 1.0
CG D:HIS359 4.4 26.9 1.0
C8' D:HWU1571 4.4 45.2 1.0
CG D:HIS226 4.5 28.9 1.0
O1B D:HWU1571 4.5 35.5 1.0
O1A D:HWU1571 4.6 32.7 1.0
O D:HOH2085 4.6 37.4 1.0
C3B D:HWU1571 4.9 35.5 1.0
C7' D:HWU1571 4.9 46.5 1.0
C5B D:HWU1571 4.9 36.0 1.0
C4B D:HWU1571 5.0 31.8 1.0

Manganese binding site 5 out of 6 in 4d0z

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Manganese binding site 5 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher 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 and Manganese (Higher Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1586

b:26.4
occ:1.00
 O2B E:HWU1585 2.1 32.2 1.0
O2A E:HWU1585 2.1 26.9 1.0
O E:HOH2066 2.2 31.2 1.0
OD2 E:ASP224 2.2 28.4 1.0
NE2 E:HIS226 2.3 27.9 1.0
NE2 E:HIS359 2.3 26.7 1.0
CE1 E:HIS226 3.1 27.5 1.0
CE1 E:HIS359 3.2 26.5 1.0
PB E:HWU1585 3.3 30.3 1.0
CG E:ASP224 3.3 30.0 1.0
PA E:HWU1585 3.3 29.3 1.0
CD2 E:HIS226 3.4 27.4 1.0
CD2 E:HIS359 3.4 26.8 1.0
O3A E:HWU1585 3.6 35.9 1.0
CB E:ASP224 3.8 29.4 1.0
N2' E:HWU1585 4.1 54.9 1.0
O1B E:HWU1585 4.2 43.3 1.0
O5B E:HWU1585 4.2 29.2 1.0
C5B E:HWU1585 4.2 30.5 1.0
ND1 E:HIS226 4.3 27.8 1.0
OD1 E:ASP224 4.4 33.3 1.0
ND1 E:HIS359 4.4 26.0 1.0
O E:VAL360 4.4 24.6 1.0
O1' E:HWU1585 4.4 42.7 1.0
O1A E:HWU1585 4.4 30.3 1.0
CG E:HIS226 4.5 28.0 1.0
CG E:HIS359 4.5 25.9 1.0
C8' E:HWU1585 4.5 58.4 1.0
C3B E:HWU1585 4.8 35.3 1.0
O E:HOH2104 4.8 29.2 1.0
C7' E:HWU1585 4.9 54.1 1.0
NH2 E:ARG362 4.9 39.8 1.0
C4B E:HWU1585 5.0 32.3 1.0

Manganese binding site 6 out of 6 in 4d0z

Go back to Manganese Binding Sites List in 4d0z
Manganese binding site 6 out of 6 in the Galnac-T2 Crystal Soaked with Udp-5SGALNAC, MEA2 and Manganese (Higher 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 and Manganese (Higher Resolution Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1570

b:42.3
occ:1.00
 O2A F:HWU1571 1.9 44.3 1.0
O2B F:HWU1571 2.2 47.7 1.0
OD2 F:ASP224 2.2 42.0 1.0
NE2 F:HIS226 2.2 41.4 1.0
NE2 F:HIS359 2.3 37.8 1.0
O F:HOH2041 2.4 46.4 1.0
CE1 F:HIS226 3.1 41.9 1.0
PA F:HWU1571 3.2 42.7 1.0
CE1 F:HIS359 3.2 37.9 1.0
CD2 F:HIS226 3.3 42.8 1.0
PB F:HWU1571 3.3 44.6 1.0
CG F:ASP224 3.3 42.9 1.0
CD2 F:HIS359 3.4 38.3 1.0
O3A F:HWU1571 3.6 43.3 1.0
O5B F:HWU1571 3.8 46.9 1.0
CB F:ASP224 3.8 39.5 1.0
ND1 F:HIS226 4.3 42.5 1.0
N2' F:HWU1571 4.3 56.0 1.0
O1' F:HWU1571 4.3 48.6 1.0
O F:VAL360 4.4 45.1 1.0
ND1 F:HIS359 4.4 39.0 1.0
CG F:HIS226 4.4 41.8 1.0
O1A F:HWU1571 4.4 39.0 1.0
OD1 F:ASP224 4.4 43.4 1.0
CG F:HIS359 4.5 38.3 1.0
O1B F:HWU1571 4.5 54.1 1.0
C8' F:HWU1571 4.5 60.1 1.0
O F:HOH2053 4.6 43.2 1.0
C3B F:HWU1571 4.9 43.5 1.0
C5B F:HWU1571 4.9 42.7 1.0
NH2 F:ARG362 5.0 49.0 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 18:57:34 2024

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