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Manganese in PDB 6e4q: Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+

Enzymatic activity of Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+

All present enzymatic activity of Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+:
2.4.1.41;

Protein crystallography data

The structure of Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+, PDB code: 6e4q was solved by N.L.Samara, L.A.Tabak, K.G.Ten Hagen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.80
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.286, 168.756, 153.099, 90.00, 106.28, 90.00
R / Rfree (%) 19 / 26

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+ (pdb code 6e4q). 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 the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+, PDB code: 6e4q:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6e4q

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Manganese binding site 1 out of 4 in the Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+


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 the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:46.3
occ:1.00
 O1A A:UDP703 2.1 77.7 1.0
OD2 A:ASP301 2.2 59.7 1.0
O1B A:UDP703 2.2 77.0 1.0
NE2 A:HIS437 2.3 56.3 1.0
NE2 A:HIS303 2.3 32.6 1.0
O A:HOH801 2.6 46.0 1.0
CE1 A:HIS303 3.1 38.6 1.0
CE1 A:HIS437 3.2 55.3 1.0
PB A:UDP703 3.2 63.2 1.0
CD2 A:HIS437 3.2 55.2 1.0
CD2 A:HIS303 3.3 37.2 1.0
CG A:ASP301 3.4 53.9 1.0
PA A:UDP703 3.4 69.5 1.0
O2B A:UDP703 3.5 53.2 1.0
O3A A:UDP703 3.6 67.4 1.0
CB A:ASP301 3.9 30.9 1.0
C5' A:UDP703 4.1 66.6 1.0
ND1 A:HIS303 4.2 44.3 1.0
O5' A:UDP703 4.2 68.8 1.0
ND1 A:HIS437 4.3 54.9 1.0
CG A:HIS437 4.3 46.8 1.0
CG A:HIS303 4.4 42.7 1.0
OD1 A:ASP301 4.4 62.7 1.0
O2A A:UDP703 4.5 64.3 1.0
O3B A:UDP703 4.5 50.2 1.0
O A:ILE438 4.7 46.1 1.0
NH1 A:ARG440 4.9 65.7 1.0
C3' A:UDP703 5.0 62.7 1.0

Manganese binding site 2 out of 4 in 6e4q

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Manganese binding site 2 out of 4 in the Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+


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 the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:55.8
occ:1.00
 O1B B:UDP703 2.2 77.4 1.0
OD2 B:ASP301 2.2 64.0 1.0
NE2 B:HIS303 2.2 36.8 1.0
NE2 B:HIS437 2.3 68.4 1.0
O1A B:UDP703 2.8 97.1 1.0
CE1 B:HIS303 3.1 37.2 1.0
PB B:UDP703 3.1 76.1 1.0
CE1 B:HIS437 3.1 67.4 1.0
O5' B:UDP703 3.3 87.0 1.0
CD2 B:HIS303 3.3 43.6 1.0
O3B B:UDP703 3.3 78.0 1.0
CD2 B:HIS437 3.3 62.2 1.0
CG B:ASP301 3.4 62.5 1.0
PA B:UDP703 3.4 89.9 1.0
O3A B:UDP703 3.5 79.1 1.0
CB B:ASP301 4.0 52.5 1.0
C5' B:UDP703 4.2 77.6 1.0
ND1 B:HIS303 4.2 49.6 1.0
ND1 B:HIS437 4.3 65.7 1.0
CG B:HIS303 4.3 49.4 1.0
CG B:HIS437 4.4 58.0 1.0
O2B B:UDP703 4.4 64.7 1.0
OD1 B:ASP301 4.4 67.7 1.0
O B:ILE438 4.6 63.6 1.0
O2A B:UDP703 4.9 93.4 1.0

Manganese binding site 3 out of 4 in 6e4q

Go back to Manganese Binding Sites List in 6e4q
Manganese binding site 3 out of 4 in the Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+


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 the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:54.4
occ:1.00
 NE2 C:HIS303 2.2 38.4 1.0
OD2 C:ASP301 2.2 57.4 1.0
NE2 C:HIS437 2.3 57.5 1.0
O1B C:UDP703 2.5 76.5 1.0
O2A C:UDP703 2.5 85.9 1.0
CE1 C:HIS303 3.1 45.2 1.0
PB C:UDP703 3.1 82.8 1.0
CD2 C:HIS303 3.2 41.3 1.0
O3A C:UDP703 3.2 88.7 1.0
CE1 C:HIS437 3.2 59.1 1.0
O2B C:UDP703 3.3 87.5 1.0
CG C:ASP301 3.3 58.2 1.0
PA C:UDP703 3.4 84.0 1.0
CD2 C:HIS437 3.4 53.2 1.0
CB C:ASP301 3.9 48.8 1.0
O5' C:UDP703 4.0 77.3 1.0
C5' C:UDP703 4.1 78.9 1.0
ND1 C:HIS303 4.2 49.9 1.0
CG C:HIS303 4.3 45.7 1.0
OD1 C:ASP301 4.4 68.7 1.0
ND1 C:HIS437 4.4 55.0 1.0
O C:ILE438 4.5 68.2 1.0
CG C:HIS437 4.5 50.5 1.0
O3B C:UDP703 4.6 75.1 1.0
O1A C:UDP703 4.7 87.7 1.0
C3' C:UDP703 4.8 77.6 1.0
C4' C:UDP703 5.0 78.2 1.0

Manganese binding site 4 out of 4 in 6e4q

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Manganese binding site 4 out of 4 in the Crystal Structure of the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+


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 the Drosophila Melanogaster Polypeptide N- Acetylgalactosaminyl Transferase PGANT9A in Complex with Udp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn701

b:51.4
occ:1.00
 OD2 D:ASP301 2.2 82.2 1.0
NE2 D:HIS437 2.3 60.0 1.0
NE2 D:HIS303 2.3 41.9 1.0
O3B D:UDP703 2.3 63.6 1.0
O D:HOH804 2.7 36.8 1.0
O1A D:UDP703 2.8 81.0 1.0
CE1 D:HIS303 3.1 41.2 1.0
PB D:UDP703 3.1 59.5 1.0
CE1 D:HIS437 3.2 53.6 1.0
CD2 D:HIS437 3.2 50.9 1.0
CD2 D:HIS303 3.3 50.3 1.0
O1B D:UDP703 3.3 43.5 1.0
CG D:ASP301 3.4 74.3 1.0
O3A D:UDP703 3.5 73.0 1.0
PA D:UDP703 3.7 82.0 1.0
CB D:ASP301 3.9 63.4 1.0
C5' D:UDP703 4.1 73.7 1.0
ND1 D:HIS303 4.2 49.0 1.0
ND1 D:HIS437 4.3 53.6 1.0
O5' D:UDP703 4.3 81.0 1.0
CG D:HIS437 4.3 56.0 1.0
CG D:HIS303 4.4 49.3 1.0
OD1 D:ASP301 4.4 72.3 1.0
O2B D:UDP703 4.5 45.2 1.0
O D:ILE438 4.6 53.4 1.0
O2A D:UDP703 4.9 87.3 1.0
C3' D:UDP703 5.0 75.0 1.0

Reference:

S.Ji, N.L.Samara, L.Revoredo, L.Zhang, D.T.Tran, K.Muirhead, L.A.Tabak, K.G.Ten Hagen. A Molecular Switch Orchestrates Enzyme Specificity and Secretory Granule Morphology. Nat Commun V. 9 3508 2018.
ISSN: ESSN 2041-1723
PubMed: 30158631
DOI: 10.1038/S41467-018-05978-9
Page generated: Sun Oct 6 04:18:20 2024

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