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Manganese in PDB 4njj: Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II)

Enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II)

All present enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II):
4.3.99.3;

Protein crystallography data

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II), PDB code: 4njj was solved by D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.16 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.174, 119.174, 105.310, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20

Other elements in 4njj:

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II) also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II) (pdb code 4njj). 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 Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II), PDB code: 4njj:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4njj

Go back to Manganese Binding Sites List in 4njj
Manganese binding site 1 out of 4 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II)


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 Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:76.8
occ:1.00
 N5 A:2K8303 2.0 72.5 1.0
O A:HOH416 2.3 56.0 1.0
O4 A:2K8303 2.7 75.5 1.0
C6 A:2K8303 3.0 58.6 1.0
C4A A:2K8303 3.0 70.2 1.0
O A:HOH417 3.1 65.7 1.0
O6A A:2K8303 3.1 70.1 1.0
C4 A:2K8303 3.2 65.7 1.0
OG1 A:THR51 3.4 63.2 1.0
C6A A:2K8303 3.5 53.5 1.0
NH2 A:ARG27 3.9 57.6 1.0
OD1 A:ASP50 4.1 59.9 1.0
NH1 A:ARG27 4.1 52.1 1.0
OD2 A:ASP50 4.2 59.4 1.0
C8A A:2K8303 4.3 64.7 1.0
C7 A:2K8303 4.4 57.4 1.0
CZ A:ARG27 4.4 58.3 1.0
NE2 A:HIS204 4.5 59.0 1.0
CG A:ASP50 4.5 59.6 1.0
N3 A:2K8303 4.5 60.6 1.0
CE A:SAM302 4.6 51.8 1.0
CB A:THR51 4.7 56.6 1.0
OE2 A:GLU15 4.7 51.4 1.0
O6B A:2K8303 4.7 60.5 1.0
O4' A:SAM302 4.8 52.3 1.0
C5' A:SAM302 4.9 61.4 1.0
CG2 A:THR51 4.9 45.5 1.0
N8 A:2K8303 4.9 64.1 1.0
O A:HOH418 5.0 53.5 1.0

Manganese binding site 2 out of 4 in 4njj

Go back to Manganese Binding Sites List in 4njj
Manganese binding site 2 out of 4 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II)


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 Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn305

b:0.4
occ:1.00
 OD2 A:ASP52 2.5 69.9 1.0
CG A:ASP52 3.3 69.6 1.0
CB A:ASP52 3.4 51.6 1.0
OD1 A:ASP52 4.5 70.8 1.0
NZ A:LYS6 4.5 53.6 1.0
CE A:LYS6 4.7 54.0 1.0
CA A:ASP52 4.9 53.0 1.0

Manganese binding site 3 out of 4 in 4njj

Go back to Manganese Binding Sites List in 4njj
Manganese binding site 3 out of 4 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II)


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 Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn304

b:85.8
occ:1.00
 N5 B:2K8303 2.0 66.0 1.0
O B:HOH419 2.5 58.3 1.0
O B:HOH418 2.5 53.8 1.0
O4 B:2K8303 2.8 64.7 1.0
C6 B:2K8303 3.0 63.9 1.0
C4A B:2K8303 3.0 61.2 1.0
C4 B:2K8303 3.2 59.8 1.0
O6B B:2K8303 3.3 61.7 1.0
C6A B:2K8303 3.7 57.9 1.0
OG1 B:THR51 3.7 51.3 1.0
O B:HOH429 3.8 55.6 1.0
OD1 B:ASP50 3.9 56.4 1.0
OD2 B:ASP50 4.0 59.7 1.0
NH2 B:ARG27 4.2 48.7 1.0
C7 B:2K8303 4.3 64.2 1.0
C8A B:2K8303 4.3 59.5 1.0
CG B:ASP50 4.4 52.1 1.0
NE2 B:HIS204 4.4 42.8 1.0
NH1 B:ARG27 4.5 58.2 1.0
O4' B:SAM302 4.5 57.0 1.0
OE2 B:GLU15 4.6 65.6 1.0
N3 B:2K8303 4.6 63.5 1.0
CZ B:ARG27 4.7 50.3 1.0
C5' B:SAM302 4.8 61.2 1.0
O6A B:2K8303 4.9 67.7 1.0
N8 B:2K8303 4.9 59.8 1.0
CE B:SAM302 4.9 51.4 1.0
CB B:THR51 4.9 50.9 1.0
CE1 B:HIS204 5.0 50.6 1.0

Manganese binding site 4 out of 4 in 4njj

Go back to Manganese Binding Sites List in 4njj
Manganese binding site 4 out of 4 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II)


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 Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and Manganese(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn305

b:98.3
occ:1.00
 OD2 B:ASP52 2.6 73.6 1.0
CG B:ASP52 3.4 74.1 1.0
CB B:ASP52 3.5 56.7 1.0
O B:HOH428 4.1 56.1 1.0
NZ B:LYS6 4.1 65.3 1.0
CE B:LYS6 4.4 65.7 1.0
OD1 B:ASP52 4.6 73.3 1.0
CA B:ASP52 5.0 56.7 1.0

Reference:

D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan. Radical Sam Enzyme Quee Defines A New Minimal Core Fold and Metal-Dependent Mechanism. Nat.Chem.Biol. V. 10 106 2014.
ISSN: ISSN 1552-4450
PubMed: 24362703
DOI: 10.1038/NCHEMBIO.1426
Page generated: Sat Oct 5 20:33:47 2024

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