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Manganese in PDB 7bop: Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form

Protein crystallography data

The structure of Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form, PDB code: 7bop was solved by D.Hira, T.Onoue, T.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.82 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 154.504, 273.006, 186.279, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.1

Other elements in 7bop:

The structure of Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form also contains other interesting chemical elements:

Sodium (Na) 7 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form (pdb code 7bop). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form, PDB code: 7bop:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7bop

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Manganese binding site 1 out of 6 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:44.0
occ:1.00
 O2B A:GDP402 1.9 47.7 1.0
O2A A:GDP402 2.0 48.7 1.0
OE2 A:GLU205 2.0 40.7 1.0
NE2 A:HIS354 2.1 37.9 1.0
O A:HOH730 2.3 43.1 1.0
O A:HOH600 2.4 41.6 1.0
CE1 A:HIS354 3.0 36.9 1.0
PB A:GDP402 3.2 50.8 1.0
CD2 A:HIS354 3.2 37.5 1.0
CD A:GLU205 3.2 38.7 1.0
PA A:GDP402 3.3 48.1 1.0
O3A A:GDP402 3.7 49.2 1.0
O1B A:GDP402 3.7 50.6 1.0
OE1 A:GLU205 4.0 38.6 1.0
O A:HOH546 4.0 58.2 1.0
ND1 A:HIS354 4.2 36.3 1.0
C5' A:GDP402 4.2 46.6 1.0
O A:HOH647 4.3 52.6 1.0
O5' A:GDP402 4.3 46.0 1.0
CG A:HIS354 4.3 34.4 1.0
CG A:GLU205 4.4 37.3 1.0
CB A:GLU205 4.4 35.5 1.0
O3B A:GDP402 4.5 48.8 1.0
O1A A:GDP402 4.5 47.0 1.0
C3' A:GDP402 4.6 45.4 1.0
O A:HOH828 4.7 54.5 1.0
O A:PRO206 4.9 36.3 1.0
C4' A:GDP402 4.9 46.7 1.0
CB A:ASN293 4.9 30.2 1.0

Manganese binding site 2 out of 6 in 7bop

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Manganese binding site 2 out of 6 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:42.8
occ:1.00
 O1B B:GDP402 2.0 46.6 1.0
O2A B:GDP402 2.0 47.3 1.0
OE1 B:GLU205 2.0 42.0 1.0
NE2 B:HIS354 2.1 37.4 1.0
O B:HOH701 2.3 44.8 1.0
O B:HOH537 2.4 44.3 1.0
CE1 B:HIS354 3.0 35.9 1.0
CD2 B:HIS354 3.2 37.0 1.0
CD B:GLU205 3.2 38.0 1.0
PB B:GDP402 3.2 52.1 1.0
PA B:GDP402 3.3 46.1 1.0
O3A B:GDP402 3.7 50.1 1.0
O3B B:GDP402 3.8 55.7 1.0
OE2 B:GLU205 3.9 41.0 1.0
O B:HOH606 3.9 54.0 1.0
ND1 B:HIS354 4.2 35.5 1.0
O B:HOH554 4.3 48.6 1.0
C5' B:GDP402 4.3 45.9 1.0
CG B:HIS354 4.3 34.7 1.0
O5' B:GDP402 4.3 45.8 1.0
O B:HOH529 4.4 52.7 1.0
CG B:GLU205 4.4 36.7 1.0
CB B:GLU205 4.4 34.9 1.0
O1A B:GDP402 4.5 47.6 1.0
O2B B:GDP402 4.5 51.9 1.0
O B:HOH821 4.5 56.5 1.0
C3' B:GDP402 4.6 43.6 1.0
O B:PRO206 4.8 36.4 1.0
C4' B:GDP402 5.0 45.4 1.0
CB B:ASN293 5.0 29.9 1.0

Manganese binding site 3 out of 6 in 7bop

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Manganese binding site 3 out of 6 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:45.6
occ:1.00
 O2B C:GDP402 1.9 51.0 1.0
O2A C:GDP402 2.0 46.4 1.0
OE2 C:GLU205 2.0 41.8 1.0
O C:HOH510 2.1 42.9 1.0
NE2 C:HIS354 2.1 41.8 1.0
O C:HOH526 2.3 46.7 1.0
CE1 C:HIS354 3.0 39.5 1.0
CD2 C:HIS354 3.2 39.6 1.0
PB C:GDP402 3.2 51.7 1.0
CD C:GLU205 3.3 41.4 1.0
PA C:GDP402 3.3 45.6 1.0
O3A C:GDP402 3.7 50.1 1.0
O3B C:GDP402 3.7 49.7 1.0
OE1 C:GLU205 4.0 44.7 1.0
ND1 C:HIS354 4.2 38.9 1.0
C5' C:GDP402 4.2 43.1 1.0
O5' C:GDP402 4.3 42.4 1.0
CG C:HIS354 4.3 37.3 1.0
O C:HOH505 4.4 49.7 1.0
CG C:GLU205 4.4 39.9 1.0
O1B C:GDP402 4.5 50.9 1.0
O1A C:GDP402 4.5 46.2 1.0
CB C:GLU205 4.5 38.0 1.0
C3' C:GDP402 4.6 42.1 1.0
O C:PRO206 4.8 38.5 1.0
C4' C:GDP402 5.0 42.4 1.0

Manganese binding site 4 out of 6 in 7bop

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Manganese binding site 4 out of 6 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


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 Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:44.5
occ:1.00
 O2B D:GDP402 1.9 48.5 1.0
OE2 D:GLU205 2.0 42.2 1.0
O1A D:GDP402 2.0 47.9 1.0
NE2 D:HIS354 2.1 37.8 1.0
O D:HOH525 2.3 45.6 1.0
O D:HOH664 2.4 48.9 1.0
CE1 D:HIS354 3.0 37.5 1.0
CD2 D:HIS354 3.2 37.0 1.0
CD D:GLU205 3.2 40.7 1.0
PB D:GDP402 3.2 53.8 1.0
PA D:GDP402 3.3 47.2 1.0
O3A D:GDP402 3.7 50.8 1.0
O3B D:GDP402 3.8 53.4 1.0
OE1 D:GLU205 3.9 41.9 1.0
ND1 D:HIS354 4.2 38.7 1.0
C5' D:GDP402 4.3 47.3 1.0
O5' D:GDP402 4.3 46.5 1.0
O D:HOH528 4.3 45.8 1.0
CG D:HIS354 4.3 36.2 1.0
O D:HOH687 4.4 48.1 1.0
CG D:GLU205 4.4 39.8 1.0
CB D:GLU205 4.4 37.7 1.0
O1B D:GDP402 4.5 50.8 1.0
O2A D:GDP402 4.5 47.8 1.0
C3' D:GDP402 4.6 46.0 1.0
O D:HOH789 4.7 52.2 1.0
O D:PRO206 4.8 39.6 1.0
C4' D:GDP402 5.0 47.6 1.0
CB D:ASN293 5.0 31.4 1.0

Manganese binding site 5 out of 6 in 7bop

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Manganese binding site 5 out of 6 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:49.5
occ:1.00
 O1B E:GDP402 1.9 54.2 1.0
O1A E:GDP402 1.9 51.3 1.0
OE1 E:GLU205 2.0 43.5 1.0
NE2 E:HIS354 2.1 43.7 1.0
O E:HOH565 2.2 49.8 1.0
O E:HOH555 2.4 50.4 1.0
CE1 E:HIS354 3.0 42.2 1.0
CD2 E:HIS354 3.2 42.5 1.0
PB E:GDP402 3.2 56.7 1.0
CD E:GLU205 3.3 43.5 1.0
PA E:GDP402 3.3 52.1 1.0
O3A E:GDP402 3.7 55.2 1.0
O3B E:GDP402 3.8 52.5 1.0
OE2 E:GLU205 4.0 44.1 1.0
O E:HOH594 4.1 54.1 1.0
ND1 E:HIS354 4.2 42.7 1.0
C5' E:GDP402 4.2 50.2 1.0
O5' E:GDP402 4.3 49.0 1.0
CG E:HIS354 4.3 40.9 1.0
CG E:GLU205 4.4 43.7 1.0
O E:HOH512 4.4 51.5 1.0
O2A E:GDP402 4.4 51.6 1.0
O2B E:GDP402 4.5 54.2 1.0
CB E:GLU205 4.5 42.7 1.0
C3' E:GDP402 4.6 49.4 1.0
O E:PRO206 4.9 46.2 1.0
C4' E:GDP402 4.9 49.7 1.0

Manganese binding site 6 out of 6 in 7bop

Go back to Manganese Binding Sites List in 7bop
Manganese binding site 6 out of 6 in the Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Core-Mannan Synthase A (Cmsa/KTR4) From Aspergillus Fumigatus, Mn/Gdp-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn401

b:49.8
occ:1.00
 O2B F:GDP402 1.9 54.7 1.0
OE1 F:GLU205 2.0 43.0 1.0
O2A F:GDP402 2.0 54.5 1.0
NE2 F:HIS354 2.1 42.4 1.0
O F:HOH568 2.2 43.8 1.0
O F:HOH532 2.3 50.9 1.0
CE1 F:HIS354 3.1 42.4 1.0
CD2 F:HIS354 3.2 40.5 1.0
CD F:GLU205 3.2 41.1 1.0
PB F:GDP402 3.3 54.3 1.0
PA F:GDP402 3.3 53.5 1.0
O3A F:GDP402 3.7 55.6 1.0
O3B F:GDP402 3.8 54.4 1.0
OE2 F:GLU205 3.9 46.1 1.0
O F:HOH576 4.1 49.3 1.0
ND1 F:HIS354 4.2 42.1 1.0
C5' F:GDP402 4.2 47.6 1.0
O5' F:GDP402 4.3 48.8 1.0
CG F:HIS354 4.3 39.0 1.0
CG F:GLU205 4.4 42.0 1.0
O F:HOH516 4.4 53.2 1.0
CB F:GLU205 4.5 40.8 1.0
O1A F:GDP402 4.5 52.8 1.0
O1B F:GDP402 4.5 55.2 1.0
C3' F:GDP402 4.7 46.8 1.0
O F:PRO206 4.8 40.8 1.0
C4' F:GDP402 4.9 46.9 1.0
CB F:ASN293 5.0 37.4 1.0

Reference:

D.Hira, T.Onoue, T.Oka. Structural Basis For the Core-Mannan Biosynthesis of Cell Wall Fungal-Type Galactomannan in Aspergillus Fumigatus . J.Biol.Chem. V. 295 15407 2020.
ISSN: ESSN 1083-351X
PubMed: 32873705
DOI: 10.1074/JBC.RA120.013742
Page generated: Sun Oct 6 08:10:20 2024

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