Calcium in PDB 8fk4: Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212

Enzymatic activity of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212

All present enzymatic activity of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212:
2.4.1.5;

Protein crystallography data

The structure of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212, PDB code: 8fk4 was solved by N.Schormann, C.Deivanayagam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.88 / 3.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 299.312, 215.766, 219.334, 90, 90, 90
R / Rfree (%) 22.4 / 25.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 (pdb code 8fk4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212, PDB code: 8fk4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8fk4

Go back to Calcium Binding Sites List in 8fk4
Calcium binding site 1 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1201

b:116.2
occ:1.00
 OD1 A:ASP933 2.4 96.4 1.0
OD2 A:ASP411 2.5 87.5 1.0
O A:ASN455 2.5 76.5 1.0
OD1 A:ASP411 2.5 78.4 1.0
O A:GLU405 2.6 70.3 1.0
OE2 A:GLU405 2.6 92.2 1.0
CG A:ASP411 2.8 87.2 1.0
CD A:GLU405 3.2 92.0 1.0
CG A:GLU405 3.4 68.7 1.0
C A:GLU405 3.6 77.4 1.0
CG A:ASP933 3.6 103.1 1.0
C A:ASN455 3.7 69.7 1.0
CA A:GLU405 4.0 76.6 1.0
O A:VAL412 4.1 82.4 1.0
OE1 A:GLU405 4.1 87.7 1.0
O A:ASP933 4.2 84.3 1.0
CA A:VAL456 4.3 61.1 1.0
CB A:GLU405 4.3 56.3 1.0
CB A:ASP411 4.3 71.1 1.0
OD2 A:ASP933 4.3 89.8 1.0
CG1 A:VAL456 4.3 71.4 1.0
N A:VAL456 4.5 71.3 1.0
CB A:ASP933 4.6 85.1 1.0
CA A:ASP933 4.7 79.8 1.0
ND2 A:ASN1023 4.7 86.1 1.0
CB A:ASN455 4.8 69.7 1.0
N A:PHE406 4.8 64.3 1.0
CA A:ASN455 4.8 63.0 1.0
C A:ASP933 4.8 83.5 1.0
ND2 A:ASN414 4.8 89.3 1.0
CB A:VAL456 4.9 55.5 1.0
CA A:ASP411 5.0 67.2 1.0

Calcium binding site 2 out of 8 in 8fk4

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Calcium binding site 2 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1201

b:94.7
occ:1.00
 OD1 B:ASP933 2.5 79.7 1.0
O B:ASN455 2.5 66.1 1.0
OD2 B:ASP411 2.5 92.2 1.0
OD1 B:ASP411 2.6 78.7 1.0
O B:GLU405 2.7 61.2 1.0
OE2 B:GLU405 2.9 91.3 1.0
CG B:ASP411 2.9 82.5 1.0
CD B:GLU405 3.4 93.9 1.0
CG B:GLU405 3.5 66.8 1.0
CG B:ASP933 3.7 88.4 1.0
C B:ASN455 3.7 68.0 1.0
C B:GLU405 3.7 65.7 1.0
O B:VAL412 4.0 96.0 1.0
CA B:GLU405 4.1 79.3 1.0
O B:ASP933 4.2 80.6 1.0
CA B:VAL456 4.2 64.0 1.0
CG1 B:VAL456 4.2 52.8 1.0
CB B:ASP411 4.4 71.9 1.0
OE1 B:GLU405 4.4 92.7 1.0
N B:VAL456 4.4 64.7 1.0
OD2 B:ASP933 4.4 88.0 1.0
CB B:GLU405 4.4 68.3 1.0
CB B:ASP933 4.6 80.1 1.0
CA B:ASP933 4.6 83.5 1.0
ND2 B:ASN414 4.7 82.7 1.0
CB B:VAL456 4.7 51.7 1.0
ND2 B:ASN1023 4.7 82.2 1.0
C B:ASP933 4.8 83.4 1.0
CA B:ASN455 4.8 61.8 1.0
CB B:ASN455 4.8 67.5 1.0
N B:VAL412 4.9 73.9 1.0
N B:PHE406 4.9 59.5 1.0
CA B:ASP411 4.9 74.5 1.0

Calcium binding site 3 out of 8 in 8fk4

Go back to Calcium Binding Sites List in 8fk4
Calcium binding site 3 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1201

b:80.8
occ:1.00
 O C:ASN455 2.5 76.3 1.0
O C:GLU405 2.5 91.0 1.0
OD1 C:ASP411 2.5 79.2 1.0
OD2 C:ASP411 2.5 77.8 1.0
OD1 C:ASP933 2.5 57.3 1.0
CG C:ASP411 2.8 88.1 1.0
OE2 C:GLU405 2.8 105.9 1.0
CD C:GLU405 3.3 102.3 1.0
CG C:GLU405 3.4 82.6 1.0
C C:GLU405 3.5 83.0 1.0
C C:ASN455 3.7 77.9 1.0
CG C:ASP933 3.8 78.0 1.0
CA C:GLU405 4.0 89.1 1.0
O C:VAL412 4.1 98.6 1.0
CA C:VAL456 4.3 78.2 1.0
CB C:GLU405 4.3 83.8 1.0
OE1 C:GLU405 4.3 115.4 1.0
O C:ASP933 4.3 82.8 1.0
CB C:ASP411 4.3 90.3 1.0
CG1 C:VAL456 4.4 71.7 1.0
N C:VAL456 4.4 80.5 1.0
OD2 C:ASP933 4.5 71.3 1.0
N C:PHE406 4.7 65.3 1.0
ND2 C:ASN1023 4.7 106.0 1.0
CB C:ASP933 4.7 89.0 1.0
CA C:ASN455 4.8 78.6 1.0
CB C:ASN455 4.8 67.5 1.0
CA C:ASP933 4.8 95.6 1.0
ND2 C:ASN414 4.8 96.5 1.0
CB C:VAL456 4.8 61.3 1.0
C C:ASP933 4.9 95.0 1.0
CA C:ASP411 5.0 92.8 1.0
N C:VAL412 5.0 88.4 1.0

Calcium binding site 4 out of 8 in 8fk4

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Calcium binding site 4 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1201

b:71.3
occ:1.00
 O D:ASN455 2.4 81.6 1.0
O D:GLU405 2.5 95.0 1.0
OD2 D:ASP411 2.5 88.4 1.0
OD1 D:ASP411 2.6 84.2 1.0
OD1 D:ASP933 2.6 75.7 1.0
CG D:ASP411 2.8 92.5 1.0
OE2 D:GLU405 2.9 120.2 1.0
CD D:GLU405 3.3 106.3 1.0
CG D:GLU405 3.3 86.2 1.0
C D:GLU405 3.5 87.4 1.0
C D:ASN455 3.7 85.4 1.0
CG D:ASP933 3.8 91.5 1.0
CA D:GLU405 3.9 93.7 1.0
O D:VAL412 4.1 86.4 1.0
CB D:GLU405 4.2 90.9 1.0
OE1 D:GLU405 4.3 97.2 1.0
CA D:VAL456 4.3 84.8 1.0
CB D:ASP411 4.3 83.4 1.0
O D:ASP933 4.4 98.9 1.0
N D:VAL456 4.4 96.7 1.0
CG1 D:VAL456 4.4 77.0 1.0
OD2 D:ASP933 4.5 91.1 1.0
N D:PHE406 4.6 81.5 1.0
ND2 D:ASN1023 4.7 111.4 1.0
CB D:ASN455 4.7 87.2 1.0
CA D:ASN455 4.7 87.4 1.0
CB D:ASP933 4.8 104.6 1.0
CA D:ASP933 4.9 99.0 1.0
CB D:VAL456 4.9 71.7 1.0
ND2 D:ASN414 5.0 109.5 1.0

Calcium binding site 5 out of 8 in 8fk4

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Calcium binding site 5 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1201

b:74.6
occ:1.00
 OD2 E:ASP411 2.4 82.7 1.0
O E:ASN455 2.5 76.9 1.0
OD1 E:ASP411 2.5 64.9 1.0
OD1 E:ASP933 2.5 61.7 1.0
O E:GLU405 2.6 67.1 1.0
CG E:ASP411 2.8 72.1 1.0
OE2 E:GLU405 2.8 92.2 1.0
CD E:GLU405 3.3 89.4 1.0
CG E:GLU405 3.4 47.4 1.0
C E:GLU405 3.6 70.0 1.0
C E:ASN455 3.7 63.8 1.0
CG E:ASP933 3.7 76.9 1.0
CA E:GLU405 4.0 79.2 1.0
O E:VAL412 4.0 90.4 1.0
O E:ASP933 4.2 74.3 1.0
CA E:VAL456 4.3 53.6 1.0
CB E:ASP411 4.3 69.9 1.0
OE1 E:GLU405 4.3 93.7 1.0
CB E:GLU405 4.3 61.4 1.0
CG1 E:VAL456 4.4 71.0 1.0
N E:VAL456 4.4 49.4 1.0
OD2 E:ASP933 4.5 75.7 1.0
ND2 E:ASN1023 4.7 78.2 1.0
CB E:ASP933 4.7 74.4 1.0
ND2 E:ASN414 4.8 88.9 1.0
CA E:ASP933 4.8 73.7 1.0
N E:PHE406 4.8 63.1 1.0
CA E:ASN455 4.8 61.8 1.0
CB E:ASN455 4.8 56.3 1.0
CB E:VAL456 4.8 68.0 1.0
C E:ASP933 4.9 75.0 1.0
CA E:ASP411 4.9 72.2 1.0
N E:VAL412 5.0 80.8 1.0

Calcium binding site 6 out of 8 in 8fk4

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Calcium binding site 6 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1201

b:68.8
occ:1.00
 OD2 F:ASP411 2.5 86.4 1.0
OD1 F:ASP411 2.5 76.6 1.0
O F:ASN455 2.5 79.7 1.0
OD1 F:ASP933 2.5 86.2 1.0
O F:GLU405 2.6 73.8 1.0
CG F:ASP411 2.8 83.3 1.0
OE2 F:GLU405 2.8 90.3 1.0
CD F:GLU405 3.3 93.4 1.0
CG F:GLU405 3.5 57.9 1.0
C F:GLU405 3.6 72.0 1.0
C F:ASN455 3.7 71.8 1.0
CG F:ASP933 3.7 92.0 1.0
O F:VAL412 4.0 98.5 1.0
CA F:GLU405 4.0 78.6 1.0
O F:ASP933 4.2 81.5 1.0
CA F:VAL456 4.2 57.2 1.0
CG1 F:VAL456 4.3 54.5 1.0
CB F:ASP411 4.3 77.7 1.0
OE1 F:GLU405 4.3 95.2 1.0
CB F:GLU405 4.3 59.0 1.0
N F:VAL456 4.4 62.5 1.0
OD2 F:ASP933 4.5 88.5 1.0
ND2 F:ASN1023 4.7 84.0 1.0
CB F:ASP933 4.7 78.7 1.0
CA F:ASP933 4.7 81.4 1.0
ND2 F:ASN414 4.7 85.1 1.0
CB F:ASN455 4.8 55.4 1.0
CB F:VAL456 4.8 52.9 1.0
N F:PHE406 4.8 62.0 1.0
CA F:ASN455 4.8 57.0 1.0
C F:ASP933 4.8 83.8 1.0
CA F:ASP411 4.9 86.5 1.0
N F:VAL412 4.9 75.6 1.0

Calcium binding site 7 out of 8 in 8fk4

Go back to Calcium Binding Sites List in 8fk4
Calcium binding site 7 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1201

b:75.8
occ:1.00
 O G:ASN455 2.4 74.3 1.0
OD1 G:ASP933 2.4 65.2 1.0
OD2 G:ASP411 2.6 76.1 1.0
O G:GLU405 2.6 94.3 1.0
OD1 G:ASP411 2.6 75.9 1.0
OE2 G:GLU405 2.9 103.2 1.0
CG G:ASP411 2.9 81.3 1.0
CD G:GLU405 3.4 95.2 1.0
CG G:GLU405 3.6 65.5 1.0
C G:ASN455 3.6 75.7 1.0
CG G:ASP933 3.6 86.7 1.0
C G:GLU405 3.6 79.0 1.0
CA G:GLU405 4.1 81.7 1.0
O G:VAL412 4.1 82.0 1.0
CA G:VAL456 4.2 67.5 1.0
CG1 G:VAL456 4.2 64.5 1.0
O G:ASP933 4.2 86.0 1.0
N G:VAL456 4.3 70.3 1.0
OD2 G:ASP933 4.3 85.2 1.0
OE1 G:GLU405 4.4 103.6 1.0
CB G:ASP411 4.4 75.8 1.0
CB G:GLU405 4.4 72.6 1.0
CB G:ASP933 4.6 85.2 1.0
CA G:ASP933 4.7 91.8 1.0
CB G:ASN455 4.7 79.8 1.0
CB G:VAL456 4.7 61.5 1.0
CA G:ASN455 4.7 75.1 1.0
ND2 G:ASN414 4.8 96.5 1.0
ND2 G:ASN1023 4.8 84.9 1.0
N G:PHE406 4.8 64.8 1.0
C G:ASP933 4.8 92.7 1.0
CA G:ASP411 5.0 77.9 1.0

Calcium binding site 8 out of 8 in 8fk4

Go back to Calcium Binding Sites List in 8fk4
Calcium binding site 8 out of 8 in the Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Catalytic Domain of Streptococcus Mutans Gtfb Complexed to Acarbose in Orthorhombic Space Group P21212 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1201

b:98.4
occ:1.00
 OD1 H:ASP933 2.4 83.8 1.0
O H:ASN455 2.5 115.1 1.0
OD1 H:ASP411 2.5 119.0 1.0
OD2 H:ASP411 2.6 111.9 1.0
O H:GLU405 2.6 129.7 1.0
CG H:ASP411 2.8 116.3 1.0
OE2 H:GLU405 3.0 144.6 1.0
CD H:GLU405 3.5 138.5 1.0
CG H:GLU405 3.6 109.8 1.0
CG H:ASP933 3.6 104.0 1.0
C H:GLU405 3.6 119.1 1.0
C H:ASN455 3.7 122.5 1.0
CA H:GLU405 4.1 123.6 1.0
O H:VAL412 4.1 108.9 1.0
O H:ASP933 4.2 106.3 1.0
CA H:VAL456 4.3 122.5 1.0
CB H:ASP411 4.3 95.7 1.0
OD2 H:ASP933 4.3 105.7 1.0
CG1 H:VAL456 4.4 110.5 1.0
OE1 H:GLU405 4.4 134.6 1.0
CB H:GLU405 4.4 123.6 1.0
N H:VAL456 4.4 133.4 1.0
CB H:ASP933 4.6 114.1 1.0
CA H:ASP933 4.6 127.6 1.0
CB H:ASN455 4.7 110.4 1.0
CA H:ASN455 4.7 112.5 1.0
C H:ASP933 4.8 130.1 1.0
N H:PHE406 4.8 106.3 1.0
ND2 H:ASN1023 4.8 129.2 1.0
ND2 H:ASN414 4.9 115.5 1.0
CB H:VAL456 4.9 101.2 1.0
CA H:ASP411 4.9 107.4 1.0
N H:VAL412 5.0 123.1 1.0

Reference:

N.Schormann, M.Patel, L.Thannickal, S.Purushotham, R.Wu, J.L.Mieher, H.Wu, C.Deivanayagam. The Catalytic Domains of Streptococcus Mutans Glucosyltransferases: A Structural Analysis Acta Crystallogr.,Sect.F V. 79 119 2023.
ISSN: ESSN 2053-230X
DOI: 10.1107/S2053230X23003199
Page generated: Wed Jul 26 13:19:05 2023

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