Manganese in PDB 7ch3: Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)

Enzymatic activity of Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)

All present enzymatic activity of Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A):
5.3.1.4;

Protein crystallography data

The structure of Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A), PDB code: 7ch3 was solved by T.P.Cao, I.Dhanasingh, J.Y.Sung, S.M.Shin, D.W.Lee, S.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.11 / 3.61
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 87.424, 113.913, 160.833, 81.08, 81.15, 88.89
R / Rfree (%) 23.2 / 28

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) (pdb code 7ch3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 18 binding sites of Manganese where determined in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A), PDB code: 7ch3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 18 in 7ch3

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Manganese binding site 1 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


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 Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:144.0
occ:1.00
 OE1 A:GLU329 1.8 135.2 1.0
OE2 A:GLU329 1.9 134.0 1.0
CD A:GLU329 2.1 136.0 1.0
OE2 A:GLU302 2.7 121.8 1.0
NE2 A:HIS445 2.9 53.2 1.0
CD2 A:HIS445 3.5 53.5 1.0
CG A:GLU329 3.5 112.7 1.0
CD A:GLU302 3.6 119.0 1.0
NE2 A:HIS346 3.6 103.7 1.0
OE1 A:GLU302 3.9 120.3 1.0
CE1 A:HIS445 3.9 56.0 1.0
CD2 A:HIS444 4.0 63.7 1.0
CD2 B:HIS128 4.2 59.1 1.0
CE1 A:HIS346 4.3 105.6 1.0
CD2 A:HIS346 4.4 103.4 1.0
CB A:GLU329 4.4 101.4 1.0
NE2 A:HIS444 4.5 61.0 1.0
CG A:HIS445 4.7 50.3 1.0
NE2 B:HIS128 4.7 58.8 1.0
ND1 A:HIS445 4.9 53.3 1.0
CG A:GLU302 4.9 112.0 1.0
CG B:HIS128 5.0 62.9 1.0

Manganese binding site 2 out of 18 in 7ch3

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Manganese binding site 2 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


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 Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:41.7
occ:1.00
 O A:GLY395 2.2 56.5 1.0
O H:GLY395 2.4 96.3 1.0
C A:GLY395 3.3 49.0 1.0
C H:GLY395 3.6 79.4 1.0
CA A:GLY395 3.8 41.4 1.0
OD2 A:ASP194 4.1 89.4 1.0
CB A:ASP194 4.1 80.6 1.0
OD2 A:ASP393 4.1 29.8 1.0
CA H:GLY395 4.2 78.9 1.0
CB H:ASP194 4.3 62.5 1.0
CG A:ASP194 4.4 86.3 1.0
CG H:ASP194 4.4 78.5 1.0
N A:ASN396 4.4 28.2 1.0
OD1 H:ASP194 4.5 85.5 1.0
N H:ASN396 4.6 41.9 1.0
OD1 A:ASP393 4.7 28.6 1.0
N A:GLY395 4.7 37.2 1.0
CA A:ASN396 4.8 32.5 1.0
CG A:ASP393 4.8 29.1 1.0
OD2 H:ASP194 4.9 83.3 1.0
CA H:ASN396 4.9 34.3 1.0
OD2 H:ASP393 5.0 61.9 1.0

Manganese binding site 3 out of 18 in 7ch3

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Manganese binding site 3 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


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 Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:97.9
occ:1.00
 OE2 B:GLU302 1.7 79.2 1.0
OE1 B:GLU329 1.9 113.1 1.0
CD B:GLU329 2.6 113.6 1.0
CE1 B:HIS445 2.6 45.2 1.0
OE2 B:GLU329 2.6 119.6 1.0
CD B:GLU302 2.8 68.1 1.0
NE2 B:HIS346 3.2 126.9 1.0
OE1 B:GLU302 3.3 69.0 1.0
NE2 B:HIS445 3.4 45.5 1.0
ND1 B:HIS445 3.6 42.5 1.0
CE1 B:HIS346 3.9 130.2 1.0
CD2 B:HIS346 4.0 127.6 1.0
CG B:GLU302 4.0 60.8 1.0
CG B:GLU329 4.0 101.1 1.0
CD2 B:HIS444 4.4 40.8 1.0
CD2 B:HIS445 4.6 42.5 1.0
CB B:GLU329 4.6 92.0 1.0
CG B:HIS445 4.7 39.5 1.0
NE2 B:HIS444 4.7 42.5 1.0
ND1 C:HIS128 4.8 75.7 1.0
CE B:MET347 4.8 113.8 1.0
ND1 B:HIS346 4.9 128.7 1.0
CE1 C:HIS128 5.0 79.2 1.0
CG B:HIS346 5.0 128.3 1.0

Manganese binding site 4 out of 18 in 7ch3

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Manganese binding site 4 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


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 Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:117.0
occ:1.00
 OE2 C:GLU302 1.9 133.6 1.0
OE2 C:GLU329 2.3 110.2 1.0
CD C:GLU302 2.7 123.9 1.0
NE2 C:HIS445 2.9 40.5 1.0
OE1 C:GLU302 2.9 132.4 1.0
OE1 C:GLU329 2.9 111.5 1.0
CD C:GLU329 2.9 107.8 1.0
CE1 C:HIS445 3.6 39.9 1.0
CD2 C:HIS445 3.9 39.7 1.0
CG C:GLU302 4.1 101.6 1.0
CD2 C:HIS444 4.2 38.8 1.0
NE2 C:HIS444 4.4 38.7 1.0
NE2 C:HIS346 4.4 100.5 1.0
CG C:GLU329 4.4 99.9 1.0
CD2 A:HIS128 4.5 73.7 1.0
CE C:MET347 4.7 120.7 1.0
ND1 C:HIS445 4.8 38.8 1.0
NE2 A:HIS128 4.9 73.4 1.0
CG C:HIS445 4.9 38.6 1.0
CE1 C:HIS346 4.9 104.0 1.0

Manganese binding site 5 out of 18 in 7ch3

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Manganese binding site 5 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


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 Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:66.1
occ:1.00
 O C:GLY395 2.3 49.4 1.0
O D:GLY395 2.3 29.7 1.0
OE1 D:GLU197 2.4 96.9 1.0
OD2 C:ASP194 3.1 59.6 1.0
C C:GLY395 3.4 42.6 1.0
C D:GLY395 3.4 29.6 1.0
CD D:GLU197 3.6 91.2 1.0
OD2 D:ASP194 3.7 69.9 1.0
CB C:ASP194 3.8 58.0 1.0
CG C:ASP194 3.9 59.8 1.0
CA D:GLY395 4.0 30.0 1.0
CA C:GLY395 4.0 38.7 1.0
OE2 D:GLU197 4.1 97.0 1.0
CB D:ASP194 4.1 66.3 1.0
CG D:ASP194 4.4 70.0 1.0
OD2 D:ASP393 4.4 33.0 1.0
OD2 C:ASP393 4.5 31.0 1.0
N C:ASN396 4.5 42.1 1.0
N D:ASN396 4.6 42.5 1.0
CG D:GLU197 4.7 73.8 1.0
CA C:ASN396 4.9 39.8 1.0
N D:GLY395 4.9 30.6 1.0
OD1 D:ASP393 4.9 32.4 1.0
CA D:ASN396 5.0 42.1 1.0
OD1 C:ASP393 5.0 29.7 1.0

Manganese binding site 6 out of 18 in 7ch3

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Manganese binding site 6 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


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 Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:71.1
occ:1.00
 OE2 D:GLU302 1.7 80.5 1.0
CD D:GLU302 2.5 78.3 1.0
OE1 D:GLU329 2.5 96.9 1.0
OE1 D:GLU302 2.6 81.2 1.0
OE2 D:GLU329 2.7 98.3 1.0
NE2 D:HIS445 2.8 43.0 1.0
CD D:GLU329 2.9 94.5 1.0
CE1 D:HIS445 3.6 42.3 1.0
CD2 D:HIS445 3.7 42.8 1.0
NE2 D:HIS346 3.9 109.1 1.0
CG D:GLU302 3.9 70.1 1.0
CD2 D:HIS444 4.2 41.7 1.0
CG D:GLU329 4.3 88.1 1.0
NE2 D:HIS444 4.4 41.3 1.0
ND1 F:HIS128 4.5 78.1 1.0
CE1 D:HIS346 4.5 108.6 1.0
CE1 F:HIS128 4.6 78.9 1.0
ND1 D:HIS445 4.7 41.5 1.0
CD2 D:HIS346 4.7 109.6 1.0
CG D:HIS445 4.8 41.8 1.0
CE D:MET347 4.9 152.0 1.0
CB D:GLU302 4.9 58.8 1.0

Manganese binding site 7 out of 18 in 7ch3

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Manganese binding site 7 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn501

b:78.6
occ:1.00
 OE2 E:GLU302 1.8 92.8 1.0
CD E:GLU302 2.4 81.7 1.0
OE1 E:GLU302 2.5 85.6 1.0
OE1 E:GLU329 2.6 71.8 1.0
OE2 E:GLU329 2.7 75.5 1.0
NE2 E:HIS445 2.9 30.0 1.0
CD E:GLU329 3.0 72.3 1.0
CE1 E:HIS445 3.6 30.2 1.0
CD2 E:HIS445 3.9 29.0 1.0
CG E:GLU302 3.9 68.6 1.0
NE2 E:HIS346 4.0 60.1 1.0
CD2 E:HIS444 4.1 36.6 1.0
NE2 E:HIS444 4.3 37.0 1.0
CG E:GLU329 4.4 71.6 1.0
ND1 G:HIS128 4.6 58.9 1.0
CD2 E:HIS346 4.7 58.5 1.0
ND1 E:HIS445 4.7 29.4 1.0
CE1 E:HIS346 4.8 56.2 1.0
CB E:GLU302 4.8 63.6 1.0
CE1 G:HIS128 4.9 57.8 1.0
CG E:HIS445 4.9 28.6 1.0

Manganese binding site 8 out of 18 in 7ch3

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Manganese binding site 8 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn502

b:51.1
occ:1.00
 O I:GLY395 2.1 57.7 1.0
O E:GLY395 2.3 45.4 1.0
OD2 I:ASP194 3.2 42.4 1.0
OE1 E:GLU197 3.2 70.6 1.0
C I:GLY395 3.3 46.6 1.0
OD2 E:ASP194 3.3 60.5 1.0
C E:GLY395 3.4 37.8 1.0
CD E:GLU197 3.9 70.9 1.0
CA I:GLY395 3.9 39.3 1.0
OE2 E:GLU197 4.0 66.8 1.0
CA E:GLY395 4.0 37.9 1.0
CB E:ASP194 4.0 49.4 1.0
CB I:ASP194 4.0 34.2 1.0
CG I:ASP194 4.1 39.9 1.0
CG E:ASP194 4.1 56.9 1.0
OD2 I:ASP393 4.2 62.0 1.0
N I:ASN396 4.3 30.7 1.0
N E:ASN396 4.5 31.2 1.0
CA I:ASN396 4.6 30.5 1.0
OD1 I:ASP393 4.7 61.7 1.0
OD2 E:ASP393 4.7 37.2 1.0
N I:GLY395 4.9 40.3 1.0
CG I:ASP393 4.9 57.5 1.0
CA E:ASN396 4.9 31.1 1.0
CG I:GLU197 4.9 54.8 1.0
N E:GLY395 5.0 37.2 1.0

Manganese binding site 9 out of 18 in 7ch3

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Manganese binding site 9 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn501

b:73.0
occ:1.00
 OE2 F:GLU302 2.1 109.5 1.0
OE2 F:GLU329 2.3 128.2 1.0
OE1 F:GLU329 2.7 127.2 1.0
CD F:GLU329 2.8 122.6 1.0
CD F:GLU302 3.0 103.8 1.0
OE1 F:GLU302 3.1 111.4 1.0
NE2 F:HIS445 3.4 48.2 1.0
CD2 F:HIS445 4.2 49.9 1.0
CE1 F:HIS445 4.3 47.1 1.0
NE2 F:HIS346 4.3 103.4 1.0
CG F:GLU329 4.3 109.2 1.0
CD2 H:HIS128 4.4 73.3 1.0
CG F:GLU302 4.4 86.8 1.0
CD2 F:HIS444 4.4 48.0 1.0
CE F:MET347 4.5 121.4 1.0
NE2 H:HIS128 4.7 74.4 1.0
NE2 F:HIS444 4.7 46.9 1.0
CE1 F:HIS346 4.8 104.1 1.0

Manganese binding site 10 out of 18 in 7ch3

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Manganese binding site 10 out of 18 in the Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn502

b:51.3
occ:1.00
 O F:GLY395 2.2 50.5 1.0
O B:GLY395 2.4 33.0 1.0
OE2 B:GLU197 3.2 109.6 1.0
OD2 F:ASP194 3.3 85.5 1.0
C F:GLY395 3.3 40.4 1.0
OE1 F:GLU197 3.4 142.3 1.0
C B:GLY395 3.5 32.7 1.0
OD2 B:ASP194 3.6 50.8 1.0
OE2 F:GLU197 3.8 143.0 1.0
CD F:GLU197 3.9 132.4 1.0
CB F:ASP194 3.9 55.8 1.0
CA F:GLY395 3.9 34.8 1.0
CB B:ASP194 4.0 52.9 1.0
CA B:GLY395 4.0 32.8 1.0
CG F:ASP194 4.0 76.7 1.0
CG B:ASP194 4.1 52.5 1.0
CD B:GLU197 4.2 97.5 1.0
OD2 F:ASP393 4.4 38.2 1.0
N F:ASN396 4.5 29.9 1.0
OD2 B:ASP393 4.6 64.0 1.0
N B:ASN396 4.6 21.8 1.0
OD1 F:ASP393 4.8 38.4 1.0
CA F:ASN396 4.8 29.7 1.0
OE1 B:GLU197 4.8 109.3 1.0
N F:GLY395 4.9 35.7 1.0
CA B:ASN396 5.0 21.7 1.0

Reference:

T.P.Cao, I.Dhanasingh, J.Y.Sung, S.M.Shin, D.W.Lee, S.H.Lee. Crystal Structure of Arabinose Isomerase From Hyper Thermophilic Bacterium Thermotoga Maritima (Tmai) Triple Mutant (K264A, E265A, K266A) To Be Published.
Page generated: Fri Nov 5 15:42:03 2021

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