Magnesium in PDB 8sa8: Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)

Enzymatic activity of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)

All present enzymatic activity of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form):
4.4.1.8;

Protein crystallography data

The structure of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form), PDB code: 8sa8 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.22 / 1.30
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.887, 131.544, 165.363, 90, 104.48, 90
R / Rfree (%) 13.1 / 15.3

Other elements in 8sa8:

The structure of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) (pdb code 8sa8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form), PDB code: 8sa8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8sa8

Go back to Magnesium Binding Sites List in 8sa8
Magnesium binding site 1 out of 6 in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:24.9
occ:1.00
 O B:HOH786 2.2 41.4 1.0
O A:HOH524 2.4 18.5 1.0
O A:HOH685 2.5 37.2 1.0
OE1 A:GLU344 2.5 24.7 0.6
OD1 B:ASN12 2.6 22.8 1.0
OE2 A:GLU344 2.7 23.9 0.6
CD A:GLU344 3.0 23.2 0.6
O A:LEU333 3.0 23.6 1.0
NH2 B:ARG15 3.5 20.6 0.6
CG B:ASN12 3.5 19.3 1.0
ND2 B:ASN12 3.8 20.6 1.0
C A:LEU333 4.0 19.5 1.0
OG A:SER335 4.2 19.9 0.8
NH1 B:ARG15 4.2 17.2 0.4
O B:HOH713 4.2 37.3 1.0
CA A:LEU333 4.3 17.3 1.0
NH2 B:ARG15 4.4 17.2 0.4
CG A:GLU344 4.5 21.2 0.6
O B:HOH502 4.5 41.3 1.0
OE2 A:GLU378 4.5 15.5 1.0
CZ B:ARG15 4.7 19.7 0.6
CZ B:ARG15 4.7 17.7 0.4
O A:SER332 4.7 20.1 1.0
CB A:GLU344 4.8 14.7 0.4
CB B:ASN12 4.9 17.6 1.0

Magnesium binding site 2 out of 6 in 8sa8

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Magnesium binding site 2 out of 6 in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg410

b:23.3
occ:1.00
 O B:HOH606 2.3 29.3 1.0
OD1 A:ASN12 2.4 20.2 1.0
O A:HOH763 2.4 36.8 1.0
O B:HOH568 2.4 18.5 1.0
OE2 B:GLU344 2.6 33.5 1.0
OE1 B:GLU344 2.7 31.8 1.0
O B:LEU333 3.0 23.2 1.0
CD B:GLU344 3.0 30.5 1.0
CG A:ASN12 3.4 17.2 1.0
ND2 A:ASN12 3.8 20.3 1.0
NH2 A:ARG15 3.8 19.0 0.5
C B:LEU333 3.9 19.9 1.0
NH1 A:ARG15 4.2 15.7 0.5
OG B:SER335 4.2 21.0 0.8
CA B:LEU333 4.2 18.6 1.0
O A:HOH722 4.2 33.8 1.0
NH2 A:ARG15 4.4 15.5 0.5
CG B:GLU344 4.5 26.1 1.0
O B:SER332 4.6 22.1 1.0
O A:HOH503 4.6 36.4 1.0
OE2 B:GLU378 4.7 16.6 1.0
CB A:ASN12 4.7 15.3 1.0
CZ A:ARG15 4.7 15.6 0.5
CZ A:ARG15 4.9 17.7 0.5
O B:HOH753 4.9 39.0 1.0

Magnesium binding site 3 out of 6 in 8sa8

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Magnesium binding site 3 out of 6 in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg411

b:39.8
occ:1.00
 O B:HOH513 2.0 23.8 1.0
O B:HOH834 2.2 34.8 1.0
OD2 B:ASP321 4.0 24.5 1.0

Magnesium binding site 4 out of 6 in 8sa8

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Magnesium binding site 4 out of 6 in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg413

b:24.4
occ:1.00
 O C:HOH537 2.4 16.9 1.0
OD1 D:ASN12 2.4 20.8 1.0
O D:HOH815 2.4 42.0 1.0
O C:HOH658 2.5 27.6 1.0
OE1 C:GLU344 2.5 24.0 0.6
OE2 C:GLU344 2.6 24.0 0.6
CD C:GLU344 2.9 23.1 0.6
O C:LEU333 3.0 23.5 1.0
CG D:ASN12 3.4 16.5 1.0
ND2 D:ASN12 3.8 17.6 1.0
NH2 D:ARG15 3.8 20.9 0.6
C C:LEU333 4.0 20.1 1.0
NH1 D:ARG15 4.0 18.4 0.4
OG C:SER335 4.1 20.7 0.7
O D:HOH708 4.2 37.6 1.0
CA C:LEU333 4.3 18.6 1.0
CG C:GLU344 4.5 21.2 0.6
NH2 D:ARG15 4.5 16.9 0.4
OE2 C:GLU378 4.6 15.5 1.0
O D:HOH503 4.6 37.3 1.0
O C:SER332 4.7 21.2 1.0
CZ D:ARG15 4.7 17.3 0.4
CB D:ASN12 4.7 14.8 1.0
CB C:GLU344 4.8 15.9 0.4
CZ D:ARG15 4.8 19.6 0.6
O C:HOH772 4.8 40.6 1.0
OG C:SER335 4.9 15.8 0.3

Magnesium binding site 5 out of 6 in 8sa8

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Magnesium binding site 5 out of 6 in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg413

b:26.8
occ:1.00
 O C:HOH811 2.4 40.5 1.0
O D:HOH529 2.4 18.5 1.0
O D:HOH513 2.4 40.5 1.0
O D:HOH635 2.5 31.9 1.0
OD1 C:ASN12 2.5 22.2 1.0
OE1 D:GLU344 2.5 26.9 0.6
OE2 D:GLU344 2.8 25.3 0.6
CD D:GLU344 3.0 24.8 0.6
O D:LEU333 3.0 24.1 1.0
CG C:ASN12 3.5 18.1 1.0
NH2 C:ARG15 3.6 20.0 0.5
ND2 C:ASN12 3.8 21.0 1.0
C D:LEU333 4.0 19.8 1.0
O C:HOH760 4.1 43.9 1.0
OG D:SER335 4.2 19.5 0.7
NH1 C:ARG15 4.2 16.9 0.5
CA D:LEU333 4.2 17.7 1.0
NH2 C:ARG15 4.4 18.0 0.5
O C:HOH506 4.4 41.6 1.0
CG D:GLU344 4.5 22.0 0.6
OE2 D:GLU378 4.6 15.8 1.0
O D:SER332 4.7 21.2 1.0
CZ C:ARG15 4.7 19.0 0.5
CZ C:ARG15 4.7 17.8 0.5
CB D:GLU344 4.8 15.8 0.4
CB C:ASN12 4.8 16.1 1.0
OG D:SER335 5.0 15.0 0.3

Magnesium binding site 6 out of 6 in 8sa8

Go back to Magnesium Binding Sites List in 8sa8
Magnesium binding site 6 out of 6 in the Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes, Covalently Bound and Free Plp (I2 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg414

b:48.1
occ:1.00
 O D:HOH701 2.2 33.4 1.0
O D:HOH610 2.2 31.2 1.0
O D:HOH869 2.4 36.1 1.0
O D:LEU54 3.0 15.1 1.0
O D:VAL35 3.6 18.5 1.0
CD1 D:PHE36 3.6 15.0 1.0
CE1 D:PHE36 3.8 15.7 1.0
CB D:LEU54 3.8 12.5 1.0
C D:LEU54 3.9 12.3 1.0
O D:HOH713 4.3 20.9 1.0
C D:VAL35 4.3 14.7 1.0
CA D:LEU54 4.4 12.3 1.0
CB D:ALA45 4.5 15.3 1.0
O D:HOH655 4.5 27.6 1.0
O D:HOH549 4.6 25.1 1.0
CA D:PHE36 4.6 14.2 1.0
CG D:PHE36 4.7 14.4 1.0
N D:PHE36 4.8 13.7 1.0
N D:LEU54 4.8 13.1 1.0
N D:PHE55 4.9 11.7 1.0
N D:VAL35 4.9 13.2 1.0
CB D:LEU34 5.0 12.1 1.0

Reference:

L.Liu, S.Lovell, K.P.Battaile, A.Cooper. Crystal Structure of Cystathionine Beta Lyase From Klebsiella Aerogenes (I2 Form) To Be Published.
Page generated: Fri Oct 4 19:18:12 2024

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