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Manganese in PDB 5t2k: Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III

Protein crystallography data

The structure of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III, PDB code: 5t2k was solved by G.H.Gauss, A.I.Celis, J.L.Dubois, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.40 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.016, 93.458, 132.543, 90.00, 105.31, 90.00
R / Rfree (%) 15.4 / 17.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III (pdb code 5t2k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III, PDB code: 5t2k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 5t2k

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Manganese binding site 1 out of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:19.2
occ:1.00
MN A:76R301 0.0 19.2 1.0
NB A:76R301 2.1 23.6 1.0
ND A:76R301 2.1 21.3 1.0
NA A:76R301 2.1 20.7 1.0
NC A:76R301 2.1 20.8 1.0
NE2 A:HIS171 2.3 17.9 1.0
C4B A:76R301 3.1 18.8 1.0
C4D A:76R301 3.1 22.3 1.0
C1A A:76R301 3.1 24.4 1.0
C1C A:76R301 3.1 17.8 1.0
C1D A:76R301 3.1 23.1 1.0
C4A A:76R301 3.1 16.6 1.0
C4C A:76R301 3.1 18.7 1.0
C1B A:76R301 3.1 19.0 1.0
CD2 A:HIS171 3.3 17.5 1.0
CE1 A:HIS171 3.4 20.4 1.0
HD2 A:HIS171 3.4 21.0 1.0
CHC A:76R301 3.5 16.6 1.0
CHA A:76R301 3.5 21.8 1.0
CHD A:76R301 3.5 19.8 1.0
CHB A:76R301 3.5 18.4 1.0
HE1 A:HIS171 3.5 24.4 1.0
HG13 A:ILE186 3.7 20.0 1.0
HG3 A:GLN184 3.8 29.1 1.0
HE1 A:MET216 4.0 22.9 1.0
HD11 A:ILE186 4.0 25.8 1.0
C3B A:76R301 4.3 17.1 1.0
C2B A:76R301 4.4 20.3 1.0
C2D A:76R301 4.4 33.5 1.0
C2A A:76R301 4.4 21.7 1.0
C3D A:76R301 4.4 30.4 1.0
C2C A:76R301 4.4 18.6 1.0
C3A A:76R301 4.4 23.4 1.0
C3C A:76R301 4.4 17.8 1.0
CG A:HIS171 4.4 16.1 1.0
ND1 A:HIS171 4.5 16.6 1.0
HE1 A:MET168 4.5 26.9 1.0
CG1 A:ILE186 4.5 16.7 1.0
HHC A:76R301 4.5 20.0 1.0
HHA A:76R301 4.5 26.2 1.0
HHD A:76R301 4.5 23.8 1.0
HHB A:76R301 4.6 22.1 1.0
HG12 A:ILE186 4.6 20.0 1.0
CD1 A:ILE186 4.6 21.5 1.0
O A:HOH584 4.7 49.3 1.0
CG A:GLN184 4.8 24.2 1.0
HD12 A:ILE186 4.8 25.8 1.0
CE A:MET216 4.8 19.1 1.0
HE21 A:GLN184 4.8 38.9 1.0
HE2 A:MET216 4.9 22.9 1.0

Manganese binding site 2 out of 5 in 5t2k

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Manganese binding site 2 out of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:20.4
occ:1.00
MN B:76R301 0.0 20.4 1.0
NA B:76R301 2.1 21.0 1.0
NB B:76R301 2.1 20.6 1.0
ND B:76R301 2.1 21.5 1.0
NC B:76R301 2.1 23.6 1.0
NE2 B:HIS171 2.3 17.9 1.0
C1A B:76R301 3.0 26.1 1.0
C4A B:76R301 3.0 21.5 1.0
C4D B:76R301 3.1 29.2 1.0
C4C B:76R301 3.1 21.2 1.0
C1C B:76R301 3.1 18.6 1.0
C1D B:76R301 3.1 23.3 1.0
C4B B:76R301 3.1 18.7 1.0
C1B B:76R301 3.1 20.7 1.0
CD2 B:HIS171 3.2 17.1 1.0
CE1 B:HIS171 3.3 17.6 1.0
HD2 B:HIS171 3.4 20.5 1.0
CHA B:76R301 3.4 23.8 1.0
CHB B:76R301 3.5 17.9 1.0
CHD B:76R301 3.5 21.2 1.0
HE1 B:HIS171 3.5 21.1 1.0
CHC B:76R301 3.5 18.6 1.0
HG13 B:ILE186 3.8 22.3 1.0
HG3 B:GLN184 3.9 32.4 1.0
HE1 B:MET216 4.0 24.1 1.0
HD11 B:ILE186 4.1 24.6 1.0
HE1 B:MET168 4.3 25.4 1.0
C3B B:76R301 4.3 17.9 1.0
C2B B:76R301 4.3 17.1 1.0
C2A B:76R301 4.3 24.3 1.0
C3A B:76R301 4.4 20.1 1.0
C3D B:76R301 4.4 27.6 1.0
C3C B:76R301 4.4 18.6 1.0
C2C B:76R301 4.4 17.8 1.0
C2D B:76R301 4.4 29.7 1.0
ND1 B:HIS171 4.4 15.7 1.0
CG B:HIS171 4.4 15.6 1.0
O B:HOH593 4.5 35.5 1.0
HHA B:76R301 4.5 28.5 1.0
HHB B:76R301 4.5 21.5 1.0
HHC B:76R301 4.5 22.3 1.0
CG1 B:ILE186 4.5 18.6 1.0
HHD B:76R301 4.6 25.4 1.0
HE21 B:GLN184 4.6 41.8 1.0
HG12 B:ILE186 4.7 22.3 1.0
CD1 B:ILE186 4.7 20.6 1.0
CG B:GLN184 4.8 27.0 1.0
HD12 B:ILE186 4.9 24.6 1.0
CE B:MET216 4.9 20.1 1.0
HE3 B:MET168 5.0 25.4 1.0

Manganese binding site 3 out of 5 in 5t2k

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Manganese binding site 3 out of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:29.7
occ:1.00
MN C:76R301 0.0 29.7 1.0
ND C:76R301 2.1 36.5 1.0
NB C:76R301 2.1 32.6 1.0
NA C:76R301 2.1 35.5 1.0
NC C:76R301 2.1 32.7 1.0
NE2 C:HIS171 2.5 26.7 1.0
C4D C:76R301 3.0 40.0 1.0
C1A C:76R301 3.1 37.9 1.0
C4B C:76R301 3.1 26.5 1.0
C1D C:76R301 3.1 35.4 1.0
C4C C:76R301 3.1 30.8 1.0
C4A C:76R301 3.1 34.0 1.0
C1C C:76R301 3.1 26.6 1.0
C1B C:76R301 3.2 32.7 1.0
CD2 C:HIS171 3.3 27.6 1.0
HD2 C:HIS171 3.3 33.1 1.0
CHA C:76R301 3.4 35.6 1.0
CHD C:76R301 3.5 33.4 1.0
CHC C:76R301 3.5 29.6 1.0
CHB C:76R301 3.5 31.3 1.0
CE1 C:HIS171 3.5 23.9 1.0
HG13 C:ILE186 3.8 27.3 1.0
HE1 C:HIS171 3.8 28.7 1.0
HG3 C:GLN184 4.0 39.8 1.0
HD11 C:ILE186 4.0 30.8 1.0
HE1 C:MET216 4.2 36.3 1.0
HE1 C:MET168 4.2 28.0 1.0
C3B C:76R301 4.3 30.6 1.0
C3D C:76R301 4.4 43.5 1.0
C2A C:76R301 4.4 41.9 1.0
C2B C:76R301 4.4 29.7 1.0
C2D C:76R301 4.4 41.9 1.0
C3A C:76R301 4.4 35.0 1.0
O C:HOH600 4.4 43.7 1.0
C3C C:76R301 4.4 29.6 1.0
C2C C:76R301 4.4 30.2 1.0
CG C:HIS171 4.5 25.8 1.0
HHA C:76R301 4.5 42.7 1.0
CG1 C:ILE186 4.5 22.7 1.0
HE21 C:GLN184 4.5 43.2 1.0
HHC C:76R301 4.5 35.6 1.0
HHD C:76R301 4.5 40.0 1.0
ND1 C:HIS171 4.6 23.0 1.0
HHB C:76R301 4.6 37.5 1.0
HG12 C:ILE186 4.6 27.3 1.0
CD1 C:ILE186 4.6 25.6 1.0
HD12 C:ILE186 4.8 30.8 1.0
CG C:GLN184 4.9 33.2 1.0
HE3 C:MET168 4.9 28.0 1.0
CE C:MET168 4.9 23.3 1.0
NE2 C:GLN184 5.0 36.0 1.0

Manganese binding site 4 out of 5 in 5t2k

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Manganese binding site 4 out of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:25.3
occ:1.00
MN D:76R301 0.0 25.3 1.0
NB D:76R301 2.1 27.6 1.0
NA D:76R301 2.1 32.5 1.0
ND D:76R301 2.1 31.5 1.0
NC D:76R301 2.1 23.3 1.0
NE2 D:HIS171 2.3 24.9 1.0
C4D D:76R301 3.1 34.0 1.0
C1A D:76R301 3.1 37.3 1.0
C4B D:76R301 3.1 23.6 1.0
C4A D:76R301 3.1 28.5 1.0
C1D D:76R301 3.1 28.8 1.0
C1C D:76R301 3.1 20.7 1.0
C4C D:76R301 3.1 23.4 1.0
C1B D:76R301 3.1 21.2 1.0
CD2 D:HIS171 3.2 21.2 1.0
HD2 D:HIS171 3.3 25.4 1.0
CE1 D:HIS171 3.4 21.9 1.0
CHA D:76R301 3.4 35.6 1.0
CHC D:76R301 3.5 19.6 1.0
CHD D:76R301 3.5 26.6 1.0
CHB D:76R301 3.5 24.9 1.0
HE1 D:HIS171 3.6 26.2 1.0
HG13 D:ILE186 3.7 25.3 1.0
HG3 D:GLN184 3.8 37.5 1.0
HD11 D:ILE186 3.9 30.7 1.0
HE1 D:MET216 4.0 33.6 1.0
C3B D:76R301 4.3 24.1 1.0
HE1 D:MET168 4.3 28.8 1.0
C2B D:76R301 4.3 22.2 1.0
C3D D:76R301 4.4 33.9 1.0
C2A D:76R301 4.4 35.6 1.0
C3A D:76R301 4.4 31.5 1.0
C2D D:76R301 4.4 38.9 1.0
CG D:HIS171 4.4 21.5 1.0
C3C D:76R301 4.4 22.4 1.0
C2C D:76R301 4.4 20.9 1.0
CG1 D:ILE186 4.4 21.1 1.0
ND1 D:HIS171 4.5 22.6 1.0
HHA D:76R301 4.5 42.8 1.0
HHC D:76R301 4.5 23.5 1.0
CD1 D:ILE186 4.5 25.6 1.0
HHB D:76R301 4.6 29.9 1.0
HHD D:76R301 4.6 32.0 1.0
HG12 D:ILE186 4.6 25.3 1.0
HD12 D:ILE186 4.7 30.7 1.0
CG D:GLN184 4.8 31.2 1.0
HE21 D:GLN184 4.8 47.0 1.0
CE D:MET216 4.9 28.0 1.0
HE3 D:MET168 5.0 28.8 1.0
HBB1 D:76R301 5.0 44.5 1.0

Manganese binding site 5 out of 5 in 5t2k

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Manganese binding site 5 out of 5 in the Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Geobacillus Stearothermophilus Hemq with Manganese-Coproporphyrin III within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:21.9
occ:1.00
MN E:76R301 0.0 21.9 1.0
NC E:76R301 2.1 24.1 1.0
NB E:76R301 2.1 21.8 1.0
NA E:76R301 2.1 22.0 1.0
ND E:76R301 2.1 24.6 1.0
NE2 E:HIS171 2.3 22.4 1.0
C1C E:76R301 3.1 19.5 1.0
C4B E:76R301 3.1 20.7 1.0
C1A E:76R301 3.1 26.1 1.0
C4C E:76R301 3.1 24.0 1.0
C4D E:76R301 3.1 28.0 1.0
C4A E:76R301 3.1 23.1 1.0
C1D E:76R301 3.1 25.0 1.0
C1B E:76R301 3.1 22.5 1.0
CD2 E:HIS171 3.2 19.8 1.0
CE1 E:HIS171 3.3 20.7 1.0
HD2 E:HIS171 3.3 23.8 1.0
CHC E:76R301 3.5 21.9 1.0
CHA E:76R301 3.5 24.4 1.0
CHD E:76R301 3.5 23.6 1.0
HE1 E:HIS171 3.5 24.8 1.0
CHB E:76R301 3.5 22.0 1.0
HG13 E:ILE186 3.8 28.3 1.0
HG3 E:GLN184 3.8 32.6 1.0
HE1 E:MET216 4.0 25.8 1.0
HD11 E:ILE186 4.0 27.6 1.0
C3B E:76R301 4.3 21.4 1.0
C2B E:76R301 4.4 15.7 1.0
C3C E:76R301 4.4 22.4 1.0
C2C E:76R301 4.4 20.7 1.0
C2A E:76R301 4.4 25.9 1.0
CG E:HIS171 4.4 18.4 1.0
ND1 E:HIS171 4.4 19.8 1.0
C3D E:76R301 4.4 36.1 1.0
C2D E:76R301 4.4 36.1 1.0
C3A E:76R301 4.4 23.0 1.0
CG1 E:ILE186 4.5 23.6 1.0
HHC E:76R301 4.5 26.3 1.0
HE1 E:MET168 4.5 26.6 1.0
HHA E:76R301 4.5 29.3 1.0
HHD E:76R301 4.6 28.3 1.0
HHB E:76R301 4.6 26.4 1.0
HG12 E:ILE186 4.6 28.3 1.0
CD1 E:ILE186 4.7 23.0 1.0
O E:HOH599 4.7 48.5 1.0
CG E:GLN184 4.8 27.2 1.0
CE E:MET216 4.8 21.5 1.0
HD12 E:ILE186 4.8 27.6 1.0
HE21 E:GLN184 5.0 41.6 1.0
HE2 E:MET216 5.0 25.8 1.0

Reference:

A.I.Celis, G.H.Gauss, B.R.Streit, K.Shisler, G.C.Moraski, K.R.Rodgers, G.S.Lukat-Rodgers, J.W.Peters, J.L.Dubois. Structure-Based Mechanism For Oxidative Decarboxylation Reactions Mediated By Amino Acids and Heme Propionates in Coproheme Decarboxylase (Hemq). J. Am. Chem. Soc. 2017.
ISSN: ESSN 1520-5126
PubMed: 27936663
DOI: 10.1021/JACS.6B11324
Page generated: Sun Oct 6 02:54:49 2024

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